NAMD-L: By Thread
By Thread
3455 messages sorted by:
[ author ]
[ date ]
[ subject ]
[ attachment ]
About this archive
Starting: Sat Jan 01 2005 - 14:57:24 CST
Ending: Fri Dec 29 2006 - 23:10:16 CST
- compute nonbonding interactions on bonded atoms Lorant Janosi (Fri Dec 29 2006 - 23:10:12 CST)
- unequal PMEGridSizes Neelanjana Sengupta (Fri Dec 29 2006 - 16:46:56 CST)
- namd question _at_huji.ac.il (Tue Dec 26 2006 - 04:44:42 CST)
- forming disulfide after equilibrating system dora guzman (Fri Dec 22 2006 - 17:24:10 CST)
- PME for a hexagonal system dimka (Fri Dec 22 2006 - 15:17:16 CST)
- loadforces problem Arturas Ziemys (Thu Dec 21 2006 - 13:58:44 CST)
- Simulating the orientation of detergent and lipid molecules around a membrane protein, bacteriorhodopsin Nathan H. Cho (Wed Dec 20 2006 - 20:59:20 CST)
- (no subject) Marcelo Puiatti (Wed Dec 20 2006 - 12:30:55 CST)
- NAMD constraint force and energy Floris Buelens (Wed Dec 20 2006 - 04:53:12 CST)
- g(r) Ayþe Özlem Sezerman (Wed Dec 20 2006 - 04:20:51 CST)
- about counterions taojinwuhan_at_sohu.com (Tue Dec 19 2006 - 21:18:19 CST)
- net translation in long simulations Mehdi Bagheri-Hamaneh (Tue Dec 19 2006 - 17:00:59 CST)
- Update on NAMD on BlueGene/TCL Joshua D. Moore (Tue Dec 19 2006 - 15:20:47 CST)
- ZeroMomentum-Please help Mehdi Bagheri-Hamaneh (Tue Dec 19 2006 - 08:20:04 CST)
- ZeroMomentum Mehdi Bagheri-Hamaneh (Mon Dec 18 2006 - 11:09:20 CST)
- simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Mon Dec 18 2006 - 10:16:08 CST)
- outputPressure Morad Alawneh (Fri Dec 15 2006 - 20:50:13 CST)
- Building PDB files for DNA. Wang, Boyang (Fri Dec 15 2006 - 10:29:55 CST)
- addforce Arturas Ziemys (Wed Dec 13 2006 - 14:16:43 CST)
- problems of RATTLE with big systems regafan_at_usc.es (Wed Dec 13 2006 - 12:46:22 CST)
- Problem with equilibration and pressure Jacob Poehlsgaard (Wed Dec 13 2006 - 05:31:49 CST)
- simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Wed Dec 13 2006 - 02:01:41 CST)
- Re: simulation of membrane-protein systems Peter Freddolino (Wed Dec 13 2006 - 07:49:30 CST)
- Re: simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Wed Dec 13 2006 - 08:23:15 CST)
- Re: simulation of membrane-protein systems Peter Freddolino (Wed Dec 13 2006 - 08:25:07 CST)
- Re: simulation of membrane-protein systems Cesar Luis Avila (Wed Dec 13 2006 - 09:14:07 CST)
- Re: simulation of membrane-protein systems Marcos Sotomayor (Wed Dec 13 2006 - 11:02:37 CST)
- Re: simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Wed Dec 13 2006 - 11:12:13 CST)
- Re: simulation of membrane-protein systems Peter Freddolino (Wed Dec 13 2006 - 11:16:21 CST)
- Re: simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Wed Dec 13 2006 - 11:19:01 CST)
- Re: simulation of membrane-protein systems Peter Freddolino (Wed Dec 13 2006 - 11:30:51 CST)
- Re: simulation of membrane-protein systems regafan_at_usc.es (Wed Dec 13 2006 - 13:47:44 CST)
- Re: simulation of membrane-protein systems JC Gumbart (Wed Dec 13 2006 - 13:59:27 CST)
- Re: simulation of membrane-protein systems Marcos Sotomayor (Wed Dec 13 2006 - 11:34:22 CST)
- Re: simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Wed Dec 13 2006 - 11:38:11 CST)
- Re: simulation of membrane-protein systems Marcos Sotomayor (Wed Dec 13 2006 - 11:59:53 CST)
- Re: simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Fri Dec 15 2006 - 02:24:01 CST)
- Re: simulation of membrane-protein systems Richard Wood (Wed Dec 13 2006 - 14:21:25 CST)
- Re: simulation of membrane-protein systems JC Gumbart (Wed Dec 13 2006 - 14:42:24 CST)
- Re: simulation of membrane-protein systems Guo Zhi (Wed Dec 13 2006 - 22:00:03 CST)
- RE: simulation of membrane-protein systems JC Gumbart (Wed Dec 13 2006 - 22:28:17 CST)
- Parallelization method Jordi Camps (Thu Dec 14 2006 - 11:33:38 CST)
- Re: Parallelization method JC Gumbart (Thu Dec 14 2006 - 11:45:45 CST)
- RE: Parallelization method Jordi Camps (Thu Dec 14 2006 - 12:04:34 CST)
- Re: simulation of membrane-protein systems Richard Wood (Fri Dec 15 2006 - 05:12:26 CST)
- Re: simulation of membrane-protein systems L. Michel Espinoza-Fonseca (Wed Dec 13 2006 - 08:23:15 CST)
- Re: simulation of membrane-protein systems Peter Freddolino (Wed Dec 13 2006 - 07:49:30 CST)
- Correlation Functions Juan Diaz (Tue Dec 12 2006 - 14:39:52 CST)
- Correlation Functions Juan Diaz (Tue Dec 12 2006 - 14:24:47 CST)
- FEP & different ligands satya work (Mon Dec 11 2006 - 01:20:06 CST)
- how to use reaction field in NAMD xiaojing gong (Sun Dec 10 2006 - 21:21:33 CST)
- problem reading topolgy files Annalisa Marsico (Sun Dec 10 2006 - 06:14:51 CST)
- Re: bug in pressure calculation with E field? Peter Freddolino (Sat Dec 09 2006 - 14:19:01 CST)
- particle access in tclBC Arturas Ziemys (Thu Dec 07 2006 - 13:24:05 CST)
- Tcl_Forces / 'loadcoords' loads NOT wrapped coordinates ? Arturas Ziemys (Thu Dec 07 2006 - 12:19:31 CST)
- Help. Parameters for PSGL needed Cesar Luis Avila (Thu Dec 07 2006 - 09:49:48 CST)
- Reassigning Velocities AYTUG TUNCEL (Thu Dec 07 2006 - 06:47:58 CST)
- NAMD pairInteraction - huge VDW and TOTAL3 Ravinder Abrol (Wed Dec 06 2006 - 18:10:23 CST)
- minimization temperature and constraints AYTUG TUNCEL (Tue Dec 05 2006 - 17:20:22 CST)
- Re: Tcl_Forces = pressure shifts while Langevin Piston is ON Arturas Ziemys (Tue Dec 05 2006 - 13:47:08 CST)
- polyethylene topology Arturas Ziemys (Tue Dec 05 2006 - 12:05:57 CST)
- NAMD-2.6 Insatallation help bertrand russell (Tue Dec 05 2006 - 04:29:43 CST)
- Re: RE: about topology generation Sting (Tue Dec 05 2006 - 01:03:56 CST)
- about topology generation Sting (Mon Dec 04 2006 - 22:18:26 CST)
- Issue with rhombic dodecahedron / CHARMM compatibility Dan Bolintineanu (Mon Dec 04 2006 - 17:03:21 CST)
- Is it equilibrated? taojinwuhan_at_sohu.com (Mon Dec 04 2006 - 01:45:49 CST)
- question about RMSD defined in NAMD Boyang Wang (Sat Dec 02 2006 - 19:46:40 CST)
- Tcl_Forces = pressure shifts while Langevin Piston is ON Arturas Ziemys (Fri Dec 01 2006 - 16:53:01 CST)
- FixedAtomForces and ExcludeFromPressure Vishal Kopardé (Thu Nov 30 2006 - 19:39:49 CST)
- water box deformation AYTUG TUNCEL (Thu Nov 30 2006 - 16:59:15 CST)
- high vdw energy AYTUG TUNCEL (Thu Nov 30 2006 - 16:44:39 CST)
- getbond (Tcl forces) / PBC Arturas Ziemys (Thu Nov 30 2006 - 10:12:32 CST)
- Generalized solvent boundary potential or similar tricks for huge systems in NAMD?? Jacob Poehlsgaard (Thu Nov 30 2006 - 03:15:35 CST)
- problem w/ free energy perturbation OMAR NABEEL ALY DEMERDASH (Wed Nov 29 2006 - 18:51:17 CST)
- RATTLE errors in equilibration regafan_at_usc.es (Wed Nov 29 2006 - 09:46:32 CST)
- is there any maximum limt of atom numbers in VMD or NAMD? youbin tu (Tue Nov 28 2006 - 23:00:41 CST)
- RE: pressure calculation in applied field Todd Trimble (Tue Nov 28 2006 - 17:18:24 CST)
- Re: pressure calculation in applied field Brian Bennion (Tue Nov 28 2006 - 16:06:10 CST)
- protein unfolding -- Phi MD Wei Fu (Tue Nov 28 2006 - 13:59:29 CST)
- pressure calculation in applied field Todd Trimble (Tue Nov 28 2006 - 12:36:51 CST)
- TIP4P water Vishal Kopardé (Mon Nov 27 2006 - 17:53:34 CST)
- error message in free energy pert. OMAR NABEEL ALY DEMERDASH (Sun Nov 26 2006 - 23:36:23 CST)
- help:autopsf changed the structure! taojinwuhan_at_sohu.com (Sun Nov 26 2006 - 19:57:42 CST)
- Harmonic Constraint: 2 types Morad Alawneh (Sun Nov 26 2006 - 19:36:15 CST)
- ABF with z-coord Ugur Akgun (Fri Nov 24 2006 - 20:31:06 CST)
- dcd file format Leandro Martínez (Fri Nov 24 2006 - 05:38:05 CST)
- problems with paralellism Leandro Martínez (Thu Nov 23 2006 - 12:49:39 CST)
- Distance restraint Yao Fan (Wed Nov 22 2006 - 16:50:04 CST)
- Dummy particles Arturas Ziemys (Wed Nov 22 2006 - 14:55:36 CST)
- question on free energy pert. OMAR NABEEL ALY DEMERDASH (Wed Nov 22 2006 - 11:54:21 CST)
- LINE=*CMAP* regafan_at_usc.es (Wed Nov 22 2006 - 08:32:24 CST)
- POPC Matteo Masetti (Wed Nov 22 2006 - 04:43:08 CST)
- Re: How to create repulsive particle ? Arturas Ziemys (Tue Nov 21 2006 - 15:45:01 CST)
- electric field Todd Trimble (Tue Nov 21 2006 - 15:08:11 CST)
- How to create repulsive particle ? Arturas Ziemys (Tue Nov 21 2006 - 13:47:51 CST)
- combine.tcl Annalisa Marsico (Tue Nov 21 2006 - 12:40:00 CST)
- distorsion in hydrogens added regafan_at_usc.es (Tue Nov 21 2006 - 05:47:58 CST)
- Expansion of DCD tamal_at_iitk.ac.in (Mon Nov 20 2006 - 23:20:04 CST)
- Re: compiling charm++ with g++ 4.1 Leandro Martínez (Mon Nov 20 2006 - 14:27:43 CST)
- clustering conformations Dave Venky (Mon Nov 20 2006 - 12:42:58 CST)
- Compile charm++ with icc Shaowen Hu (Sat Nov 18 2006 - 15:42:36 CST)
- compiling charm++ with g++ 4.1 Leandro Martínez (Mon Nov 20 2006 - 10:26:22 CST)
- Tcl Boundary Forces Peter Jones (Sat Nov 18 2006 - 20:31:29 CST)
- bad exclusion count Francesco Iori (Fri Nov 17 2006 - 15:19:37 CST)
- Charged Atoms in External Magnetic Field Westley A Sherman (Thu Nov 16 2006 - 18:50:12 CST)
- electric field Todd Trimble (Thu Nov 16 2006 - 11:57:25 CST)
- strange memory behavior brian (Thu Nov 16 2006 - 11:20:06 CST)
- electric field and MISC Todd Trimble (Wed Nov 15 2006 - 18:20:54 CST)
- Re: vmd-l: PSF files append!! Neelanjana Sengupta (Wed Nov 15 2006 - 14:24:57 CST)
- small query... hl332_at_drexel.edu (Wed Nov 15 2006 - 13:48:39 CST)
- charges in topology regafan_at_usc.es (Wed Nov 15 2006 - 11:34:32 CST)
- NAMD on Linux IBM PowerPC JS20 Cluster sh (Wed Nov 15 2006 - 10:32:59 CST)
- RE: electric field and MISC energy Todd Trimble (Tue Nov 14 2006 - 10:46:19 CST)
- ABF (fwd) Matthew Davies (Tue Nov 14 2006 - 07:40:30 CST)
- Reproducing free energy profile for acetate-guanidinium association Grzegorz Jezierski (Tue Nov 14 2006 - 06:40:04 CST)
- unable to open charmm parameter file in Window bo baker (Tue Nov 14 2006 - 01:16:37 CST)
- electric field and MISC energy Todd Trimble (Mon Nov 13 2006 - 10:44:29 CST)
- recompiling NAMD 2.6 from sources on CentOS-3 x86_64: Charm++ failing test Tru Huynh (Mon Nov 13 2006 - 10:16:46 CST)
- LES / cLES Arturas Ziemys (Mon Nov 13 2006 - 09:40:09 CST)
- dcd file is too large taojinwuhan_at_sohu.com (Mon Nov 13 2006 - 02:52:41 CST)
- atomlist command in matdcd Dhiraj Srivastava (Sun Nov 12 2006 - 02:20:25 CST)
- Unnatural Bond lengths Vinit Rege (Sat Nov 11 2006 - 01:56:35 CST)
- Linux HP Itanium Quadrics Alessandro Cembran (Fri Nov 10 2006 - 17:04:45 CST)
- LES : size Arturas Ziemys (Fri Nov 10 2006 - 12:09:50 CST)
- how to remove translational and rotational motion from dcd file Dhiraj Srivastava (Thu Nov 09 2006 - 14:59:28 CST)
- Question about free energy of conformation change Peiquan Chen (Thu Nov 09 2006 - 02:26:46 CST)
- electric field and MISC energy Todd Trimble (Wed Nov 08 2006 - 16:19:02 CST)
- Another question on Diffusion Vinit Rege (Wed Nov 08 2006 - 13:15:49 CST)
- System of POPC bilayer Vinit Rege (Wed Nov 08 2006 - 12:21:56 CST)
- how long is enough to heat up and equilibrate lily jin (Wed Nov 08 2006 - 11:05:37 CST)
- infinite nanotubes with PBC in NAMD? Nicolas Winter (Wed Nov 08 2006 - 10:33:11 CST)
- PME GridSize Neelanjana Sengupta (Tue Nov 07 2006 - 17:57:24 CST)
- FEP Energy very high: Mutual exclusion of atoms Nitin Bhardwaj (Tue Nov 07 2006 - 17:28:58 CST)
- Trouble with Charmm/PDB? Javad Azadi (Mon Nov 06 2006 - 23:33:21 CST)
- dissociation in NAMD sukesh shenoy (Mon Nov 06 2006 - 11:00:40 CST)
- protein is moving from center to one corner of water box. Dhiraj Srivastava (Mon Nov 06 2006 - 01:06:53 CST)
- residue name LIP ... ! Vinit Rege (Sat Nov 04 2006 - 19:52:26 CST)
- [Fwd: Re: SMD on center of mass] Peter Freddolino (Fri Nov 03 2006 - 14:05:47 CST)
- Warning: 1 processors are overloaded due to high background load Dhiraj Srivastava (Fri Nov 03 2006 - 11:30:34 CST)
- RE: deformations in a water box during equilibration in NAMD regafan_at_usc.es (Fri Nov 03 2006 - 04:28:01 CST)
- production in NVE ensemble after equilibration in NPT ensemble Dhiraj Srivastava (Thu Nov 02 2006 - 23:54:30 CST)
- ABF on a single molecule Ugur Akgun (Thu Nov 02 2006 - 14:26:11 CST)
- Re: ABF on a single molecule Chris Chipot (Sun Nov 05 2006 - 03:26:53 CST)
- Re: ABF on a single molecule Ugur Akgun (Mon Nov 06 2006 - 14:19:04 CST)
- Re: ABF on a single molecule Chris Chipot (Mon Nov 06 2006 - 15:19:17 CST)
- Re: ABF on a single molecule Ugur Akgun (Mon Nov 06 2006 - 16:33:24 CST)
- ABF - zCoord for more than one monomer Ugur Akgun (Thu Nov 09 2006 - 10:19:47 CST)
- Re: ABF - zCoord for more than one monomer Chris Chipot (Mon Nov 13 2006 - 07:47:30 CST)
- Re: ABF on a single molecule Ugur Akgun (Mon Nov 06 2006 - 14:19:04 CST)
- Re: ABF on a single molecule Chris Chipot (Sun Nov 05 2006 - 03:26:53 CST)
- external force Al-Rawi, Ahlam (Thu Nov 02 2006 - 12:16:23 CST)
- deformations in a cubic water box during equilibration in NAMD regafan_at_usc.es (Thu Nov 02 2006 - 08:52:39 CST)
- histidine protonation xiaojing gong (Thu Nov 02 2006 - 08:18:27 CST)
- urestraint for minimizations and MD (no PMF) MW Van der Kamp, School of Chemistry (Thu Nov 02 2006 - 05:46:21 CST)
- namd installation Michal Walczak (Thu Nov 02 2006 - 03:56:21 CST)
- Hydrogens collapsing Vishal Kopardé (Wed Nov 01 2006 - 21:20:50 CST)
- equilibration of protein Dhiraj Srivastava (Wed Nov 01 2006 - 12:31:17 CST)
- rmsd is not stabilizing even after 0.6 ns Dhiraj Srivastava (Tue Oct 31 2006 - 13:41:54 CST)
- namd/charm infiniband build Rene Salmon (Mon Oct 30 2006 - 14:57:30 CST)
- Using NBFIX sukesh shenoy (Sat Oct 28 2006 - 17:59:52 CDT)
- compiling namd Michal Walczak (Sat Oct 28 2006 - 09:43:11 CDT)
- useFlexibleCell olga hrydziuszko (Sat Oct 28 2006 - 09:19:03 CDT)
- changing parameter files during simulation run sukesh shenoy (Fri Oct 27 2006 - 10:18:55 CDT)
- constrained simulation Dhiraj Srivastava (Fri Oct 27 2006 - 03:32:15 CDT)
- Re: Fwd: GRADIENT TOLERANCE: nan Brian Bennion (Thu Oct 26 2006 - 11:29:00 CDT)
- Replica Exchange Arturas Ziemys (Thu Oct 26 2006 - 10:53:16 CDT)
- Using/converting old extended top and par files? Jacob Poehlsgaard (Thu Oct 26 2006 - 05:34:31 CDT)
- Urey-Bradley term and VDW energy Hyonseok Hwang (Wed Oct 25 2006 - 22:41:36 CDT)
- Question about ABF Gaurav Sharma (Wed Oct 25 2006 - 18:03:13 CDT)
- heat capacity: NPT vs. NVT Arturas Ziemys (Wed Oct 25 2006 - 09:53:37 CDT)
- Warnings of psfgen Vishal Kopardé (Wed Oct 25 2006 - 08:37:30 CDT)
- Question about REMD ×Þ¿¡ (Wed Oct 25 2006 - 08:37:00 CDT)
- RATTLE Error Vishal Kopardé (Wed Oct 25 2006 - 06:59:18 CDT)
- error estimate in FEP calculation jz7_at_duke.edu (Tue Oct 24 2006 - 23:18:27 CDT)
- external force Al-Rawi, Ahlam (Tue Oct 24 2006 - 17:30:43 CDT)
- NPT ensemble with Periodic boundary condition Dhiraj Srivastava (Tue Oct 24 2006 - 17:07:38 CDT)
- external force Al-Rawi, Ahlam (Tue Oct 24 2006 - 14:39:42 CDT)
- Waiting for 0-th client to connect. Leandro Martínez (Tue Oct 24 2006 - 12:50:07 CDT)
- deformed water box after heating Dhiraj Srivastava (Mon Oct 23 2006 - 21:40:37 CDT)
- running 2 jobs simutaneously? Ching Wong (Mon Oct 23 2006 - 21:14:41 CDT)
- sphericalBCk1 milton sonoda (Mon Oct 23 2006 - 19:50:01 CDT)
- Replica-Exchange MD E. Prabhu Raman (Mon Oct 23 2006 - 13:53:41 CDT)
- Equilibriation Info tamal_at_iitk.ac.in (Mon Oct 23 2006 - 13:52:14 CDT)
- Re: phi and psi dihedral restraints Neelanjana Sengupta (Mon Oct 23 2006 - 12:20:41 CDT)
- calculation of non-bonded interactions Jindal Shah (Mon Oct 23 2006 - 09:55:59 CDT)
- temperature reassignment Dhiraj Srivastava (Mon Oct 23 2006 - 03:07:28 CDT)
- target molecular moves away from water box laura (Sun Oct 22 2006 - 20:18:11 CDT)
- phi and psi dihedral restraints Neelanjana Sengupta (Sun Oct 22 2006 - 18:24:24 CDT)
- deformed water box during equilibration. Dhiraj Srivastava (Sat Oct 21 2006 - 05:13:35 CDT)
- Problem setting distance restraints MW Van der Kamp, School of Chemistry (Fri Oct 20 2006 - 07:24:04 CDT)
- adding extra ions to neutralize charge on protein Dhiraj Srivastava (Thu Oct 19 2006 - 11:42:48 CDT)
- charge on protein Dhiraj Srivastava (Wed Oct 18 2006 - 21:57:28 CDT)
- Re: Intel Woodcrest version? Jacob Poehlsgaard (Wed Oct 18 2006 - 03:01:33 CDT)
- Hydroxyproline topology Neelanjana Sengupta (Tue Oct 17 2006 - 21:15:25 CDT)
- Intel Woodcrest version? Jacob Poehlsgaard (Tue Oct 17 2006 - 05:50:16 CDT)
- Free Linux Cluster-Building Workshop - 30 Nov 2006 - 01 Dec 2006 Jim Phillips (Mon Oct 16 2006 - 16:13:52 CDT)
- rigid protein Mehdi Bagheri-Hamaneh (Mon Oct 16 2006 - 13:00:58 CDT)
- Re: rigid protein Anahita Tafvizi (Thu Oct 19 2006 - 08:21:45 CDT)
- Re: rigid protein L. Michel Espinoza-Fonseca (Thu Oct 19 2006 - 10:14:21 CDT)
- Re: rigid protein Anahita Tafvizi (Thu Oct 19 2006 - 10:23:16 CDT)
- Re: rigid protein L. Michel Espinoza-Fonseca (Thu Oct 19 2006 - 10:38:33 CDT)
- Re: rigid protein Anahita Tafvizi (Thu Oct 19 2006 - 10:50:01 CDT)
- Re: rigid protein Marcos Sotomayor (Thu Oct 19 2006 - 10:55:07 CDT)
- Re: rigid protein JC Gumbart (Thu Oct 19 2006 - 11:04:37 CDT)
- Re: rigid protein Gianluca Interlandi (Thu Oct 19 2006 - 13:12:53 CDT)
- Re: rigid protein Mark Abraham (Thu Oct 19 2006 - 10:44:27 CDT)
- Re: rigid protein Marc Baaden (Thu Oct 19 2006 - 12:29:32 CDT)
- Re: rigid protein Mark Abraham (Thu Oct 19 2006 - 20:20:09 CDT)
- Re: rigid protein Luca Bellucci (Fri Oct 20 2006 - 05:08:50 CDT)
- Re: rigid protein L. Michel Espinoza-Fonseca (Thu Oct 19 2006 - 10:14:21 CDT)
- Re: rigid protein Anahita Tafvizi (Thu Oct 19 2006 - 08:21:45 CDT)
- NAMD on Dual processor computer Dhiraj Srivastava (Sun Oct 15 2006 - 14:28:31 CDT)
- problem with reassigning temperature Dhiraj Srivastava (Sat Oct 14 2006 - 21:55:15 CDT)
- CMAP in NAMD simulation Neelanjana Sengupta (Sat Oct 14 2006 - 17:26:23 CDT)
- Multiple tclForcesScript Morad Alawneh (Sat Oct 14 2006 - 14:53:28 CDT)
- simulation in nve ensemble Dhiraj Srivastava (Fri Oct 13 2006 - 21:45:37 CDT)
- about diahedra entry in top_all22_sugar.inp bqluan (Fri Oct 13 2006 - 13:31:35 CDT)
- Comments on 'restart' simulation Pijush Ghosh (Thu Oct 12 2006 - 16:33:10 CDT)
- MD in steps Pijush Ghosh (Thu Oct 12 2006 - 11:21:39 CDT)
- "reinitvel" parameter in config file Dhiraj Srivastava (Wed Oct 11 2006 - 18:34:21 CDT)
- line too long in pdb file restart.coor Dhiraj Srivastava (Wed Oct 11 2006 - 14:28:41 CDT)
- changing velocity during simulation olga hrydziuszko (Wed Oct 11 2006 - 09:05:28 CDT)
- changing velocity during simulation olga hrydziuszko (Wed Oct 11 2006 - 08:10:17 CDT)
- equilibration at three different temperature Dhiraj Srivastava (Tue Oct 10 2006 - 18:00:52 CDT)
- popc pressure profile Allan Haldane (Tue Oct 10 2006 - 11:40:43 CDT)
- Flushing output: MPI version of NAMD on AMD64 Vani Krishna (Tue Oct 10 2006 - 00:00:31 CDT)
- Re: Re: restraining the protein not to move during equilibration Lewyn Li (Mon Oct 09 2006 - 10:52:55 CDT)
- topology & parameters for urea patrick wintrode (Mon Oct 09 2006 - 11:00:44 CDT)
- Atomic partial charge Luca Bellucci (Mon Oct 09 2006 - 05:35:36 CDT)
- restraining the protein not to move during equilibration Dhiraj Srivastava (Sun Oct 08 2006 - 23:30:39 CDT)
- dissociation of water Shenoy, Sukesh (Sun Oct 08 2006 - 18:06:56 CDT)
- restarting the simulation Dhiraj Srivastava (Sun Oct 08 2006 - 16:17:38 CDT)
- value of B column is zero Dhiraj Srivastava (Sun Oct 08 2006 - 00:34:16 CDT)
- zero kinetic energy during minimization Dhiraj Srivastava (Sun Oct 08 2006 - 00:12:39 CDT)
- problem with dihedral restraint Neelanjana Sengupta (Fri Oct 06 2006 - 16:11:43 CDT)
- reflective barrier olga hrydziuszko (Fri Oct 06 2006 - 10:49:33 CDT)
- Installation Problem bertrand russell (Fri Oct 06 2006 - 06:52:00 CDT)
- periodic boundry conditions olga hrydziuszko (Fri Oct 06 2006 - 05:58:45 CDT)
- Re: vmd-l: trace to newcartoon inconsistent display problem Cesar Luis Avila (Thu Oct 05 2006 - 15:58:11 CDT)
- forward and backward pulling curcio (Thu Oct 05 2006 - 10:59:10 CDT)
- PME processors Nicholas M Glykos (Thu Oct 05 2006 - 07:11:46 CDT)
- constraining distance Anahita Tafvizi (Wed Oct 04 2006 - 13:16:29 CDT)
- sialic acid bqluan (Tue Oct 03 2006 - 15:36:00 CDT)
- missing info from NAMD output Neelanjana Sengupta (Tue Oct 03 2006 - 14:27:08 CDT)
- NAMD timestep and numsteps santanu chatterjee (Tue Oct 03 2006 - 12:39:26 CDT)
- "Adaptive" force direction in SMD? HAMON véronique (Tue Oct 03 2006 - 10:00:28 CDT)
- SMD From Force to Free Energy Ugur Akgun (Tue Oct 03 2006 - 09:54:07 CDT)
- Re: How can I do protein complex's simulation? Dhiraj Srivastava (Mon Oct 02 2006 - 19:58:29 CDT)
- How can I do protein complex's simulation? Yuqi Liu (Mon Oct 02 2006 - 18:46:13 CDT)
- Constraining a molecule and measuring the corresponding constraint force Doug Moby (Sat Sep 30 2006 - 08:36:31 CDT)
- trajectory extension E. Prabhu Raman (Fri Sep 29 2006 - 13:39:55 CDT)
- removing bonds in psf luca (Fri Sep 29 2006 - 05:44:13 CDT)
- removing bonds in psf olga hrydziuszko (Fri Sep 29 2006 - 03:45:27 CDT)
- United Atoms in NAMD Rajan Vatassery (Fri Sep 29 2006 - 02:08:12 CDT)
- Qmeasure=22?= command Arturas Ziemys (Wed Sep 27 2006 - 16:30:24 CDT)
- FFTW problem Jyh-Shyong Ho (Wed Sep 27 2006 - 04:02:57 CDT)
- about abf ËïæÃæà (Tue Sep 26 2006 - 08:30:24 CDT)
- force calculation peach gil (Tue Sep 26 2006 - 14:03:10 CDT)
- forces calculation peach gil (Tue Sep 26 2006 - 13:12:16 CDT)
- Namd list administration Cesar Luis Avila (Tue Sep 26 2006 - 10:13:58 CDT)
- redirecting stdout to a file olga hrydziuszko (Tue Sep 26 2006 - 08:11:57 CDT)
- how add bond in psf file? Luca Bellucci (Mon Sep 25 2006 - 08:18:27 CDT)
- imprecision in table energy A. Ozlem T. Bishop (Sun Sep 24 2006 - 09:57:50 CDT)
- checkpoint software for NAMD? Dan Strahs (Thu Sep 21 2006 - 15:37:47 CDT)
- Transition state Luca Bellucci (Thu Sep 21 2006 - 03:45:49 CDT)
- NAMD installation on Cray XD1 (AMD opteron 64-bit) Vani Krishna (Wed Sep 20 2006 - 23:46:37 CDT)
- NAMD installation on Xeon64 cluster Ugur Akgun (Wed Sep 20 2006 - 16:21:16 CDT)
- NAMD installation on Xeon64 cluster Ugur Akgun (Wed Sep 20 2006 - 16:08:07 CDT)
- PBS & local (scratch) space Arturas Ziemys (Wed Sep 20 2006 - 15:42:18 CDT)
- NAMD installation on Xeon64 cluster Ugur Akgun (Wed Sep 20 2006 - 15:40:16 CDT)
- force constant from gaussian to namd Shenoy, Sukesh (Wed Sep 20 2006 - 13:44:12 CDT)
- Water Hole Jacob Poehlsgaard (Tue Sep 19 2006 - 03:00:54 CDT)
- NAMD installation on Xeon64 cluster Ugur Akgun (Mon Sep 18 2006 - 16:20:42 CDT)
- Altix Performance Tuning Alessandro Cembran (Mon Sep 18 2006 - 13:18:52 CDT)
- NAMD installation on Xeon64 cluster Ugur Akgun (Fri Sep 15 2006 - 16:50:14 CDT)
- Water outside protein surface Pijush Ghosh (Fri Sep 15 2006 - 00:06:39 CDT)
- equilibrating the system with constrained Protein Dhiraj Srivastava (Thu Sep 14 2006 - 13:12:31 CDT)
- combined QM/MM calculation with NAMD Dhiraj Srivastava (Thu Sep 14 2006 - 10:35:28 CDT)
- Urea parameter bqluan (Wed Sep 13 2006 - 21:20:05 CDT)
- load balancer, athlon 64 dual core Leandro Martínez (Wed Sep 13 2006 - 07:06:08 CDT)
- top par for NAG, BMA ? Georgios Papadopoulos (Mon Sep 11 2006 - 11:47:38 CDT)
- Recentering the box on target molecule and wraping Arturas Ziemys (Mon Sep 11 2006 - 10:39:55 CDT)
- question regarding the use of reaction coordinate "distance-com" in ABF method Anahita Tafvizi (Sun Sep 10 2006 - 12:51:46 CDT)
- History file of an ABF smiulation Anahita Tafvizi (Sat Sep 09 2006 - 13:55:58 CDT)
- parameter file name E. Prabhu Raman (Fri Sep 08 2006 - 18:46:41 CDT)
- assigning atom type for parameterization Dhiraj Srivastava (Fri Sep 08 2006 - 15:23:02 CDT)
- Constraining angles ?? tamal_at_iitk.ac.in (Fri Sep 08 2006 - 13:36:31 CDT)
- Morse potential? Shenoy, Sukesh (Thu Sep 07 2006 - 21:57:56 CDT)
- Re: clarification(s) Re: namd 2.62b FATAL ERROR: Memory allocation failed on processor 0 or higher Tom Caulfield (Thu Sep 07 2006 - 20:25:27 CDT)
- FW: Compilation problems on intel woodcrest Jacob Poehlsgaard (Thu Sep 07 2006 - 06:51:41 CDT)
- no parameter for CN8-ON6 Dhiraj Srivastava (Wed Sep 06 2006 - 19:45:59 CDT)
- Win64 version Dan Strahs (Wed Sep 06 2006 - 14:50:25 CDT)
- parameterizing novel molecule Dhiraj Srivastava (Wed Sep 06 2006 - 01:52:47 CDT)
- Unit cell information in binary output files Ben Roberts (Tue Sep 05 2006 - 22:23:13 CDT)
- help: how to scale the velocities by a factor for a subset of the system? Yong Zhang (Tue Sep 05 2006 - 21:59:25 CDT)
- Accelerating groups of atoms Cesar Luis Avila (Tue Sep 05 2006 - 15:18:59 CDT)
- atom name based paremeters E. Prabhu Raman (Tue Sep 05 2006 - 14:31:30 CDT)
- mDyne/A to kcal/mol/A2 Shenoy, Sukesh (Tue Sep 05 2006 - 14:29:59 CDT)
- mDyne/A to kcal/mol/A2 Shenoy, Sukesh (Tue Sep 05 2006 - 12:56:27 CDT)
- Re: vmd-l: imposing period boundary conditions in a simulation with a crystal Axel Kohlmeyer (Tue Sep 05 2006 - 12:00:19 CDT)
- wall clock vs secs/step metrics Brian Bennion (Tue Sep 05 2006 - 12:02:29 CDT)
- Re: DPPC.Pdb file needed Elsa S. Henriques (Tue Sep 05 2006 - 08:42:29 CDT)
- calculate potential energy from DCD file casoni\_at_libero\.it (Tue Sep 05 2006 - 07:21:57 CDT)
- DPPC.Pdb file needed Lechuga, Javier (Mon Sep 04 2006 - 11:27:49 CDT)
- minimization of a cyclic peptide with NAMD Idit Buch (Mon Sep 04 2006 - 04:22:03 CDT)
- problem with Dihedral Restraints Neelanjana Sengupta (Mon Sep 04 2006 - 01:13:44 CDT)
- namd 2.62b FATAL ERROR: Memory allocation failed on processor 0 or higher Thomas Caulfield (Sun Sep 03 2006 - 20:54:06 CDT)
- Re: CoordinateTransformation Sting (Sun Sep 03 2006 - 20:17:21 CDT)
- CoordinateTransformation Neelanjana Sengupta (Sun Sep 03 2006 - 15:34:48 CDT)
- CoordinateTransformation Neelanjana Sengupta (Sun Sep 03 2006 - 15:33:32 CDT)
- pbc_box Maria Gonzalez (Sun Sep 03 2006 - 12:49:09 CDT)
- electric field Ekta Khurana (Sat Sep 02 2006 - 20:17:21 CDT)
- Angles and dihedral generation Cesar Luis Avila (Fri Sep 01 2006 - 20:02:36 CDT)
- mechanical force calculation Gaurav Sharma (Thu Aug 31 2006 - 22:23:55 CDT)
- Minimization algorithms Per Jr. Greisen (Thu Aug 31 2006 - 11:19:19 CDT)
- Patches & psfgen Marcos Sotomayor (Thu Aug 31 2006 - 11:04:03 CDT)
- Trajectory analysis Luca Bellucci (Thu Aug 31 2006 - 08:00:49 CDT)
- mass of atoms changable? E. Prabhu Raman (Wed Aug 30 2006 - 16:19:46 CDT)
- NAMD 2.6 released Jim Phillips (Wed Aug 30 2006 - 15:18:36 CDT)
- Re: vdW parameters Jindal Shah (Wed Aug 30 2006 - 15:04:16 CDT)
- prob. with constraints Neelanjana Sengupta (Wed Aug 30 2006 - 11:08:56 CDT)
- vdW parameters Jindal Shah (Wed Aug 30 2006 - 10:38:19 CDT)
- DPPC.Pdb Lechuga, Javier (Wed Aug 30 2006 - 05:57:38 CDT)
- Counting H-bonds from a dcd file Nitin Bhardwaj (Tue Aug 29 2006 - 17:00:51 CDT)
- Fat node jonathan_at_ibt.unam.mx (Mon Aug 28 2006 - 21:02:13 CDT)
- error in loading "import hessian/charge from single point calculation" in paratool Dhiraj Srivastava (Mon Aug 28 2006 - 17:53:11 CDT)
- Using PsfGen Lechuga, Javier (Mon Aug 28 2006 - 14:29:52 CDT)
- Segmentation violation from APOA1 simulation on AMD64 Cesar Luis Avila (Mon Aug 28 2006 - 13:49:25 CDT)
- About CHARMM charge Luca Bellucci (Mon Aug 28 2006 - 04:10:45 CDT)
- Building molecule from topology file Lechuga, Javier (Sat Aug 26 2006 - 06:57:40 CDT)
- Type of force values in the tclForces script. Boyang Wang (Fri Aug 25 2006 - 11:34:44 CDT)
- Info: Adjusted background load on 11 nodes. Leandro Martínez (Fri Aug 25 2006 - 07:42:28 CDT)
- Re: Info: Adjusted background load on 11 nodes. Leandro Martínez (Fri Aug 25 2006 - 08:01:53 CDT)
- Re: Re: Info: Adjusted background load on 11 nodes. Cesar Luis Avila (Sat Aug 26 2006 - 16:40:15 CDT)
- Re: Re: Info: Adjusted background load on 11 nodes. Cesar Luis Avila (Sat Aug 26 2006 - 17:00:08 CDT)
- Re: Re: Info: Adjusted background load on 11 nodes. Leandro Martínez (Mon Aug 28 2006 - 12:21:49 CDT)
- Re: Re: Info: Adjusted background load on 11 nodes. Leandro Martínez (Tue Aug 29 2006 - 07:13:51 CDT)
- Re: Re: Info: Adjusted background load on 11 nodes. Cesar Luis Avila (Sat Aug 26 2006 - 16:40:15 CDT)
- Re: Info: Adjusted background load on 11 nodes. Leandro Martínez (Fri Aug 25 2006 - 08:01:53 CDT)
- RMSD increases after restarts, decreases at the end of run hodak_at_chips.ncsu.edu (Thu Aug 24 2006 - 17:16:03 CDT)
- SMD of TFIIB! jonas condes (Thu Aug 24 2006 - 13:57:52 CDT)
- N-methylacetamide Neelanjana Sengupta (Tue Aug 22 2006 - 19:21:39 CDT)
- charmm toppology : internal coordinates Arturas Ziemys (Tue Aug 22 2006 - 16:39:00 CDT)
- NAMD 2.6b2 on IBM POWER5 with AIX 5.3 Operating System rossi_at_york.cuny.edu (Tue Aug 22 2006 - 12:45:59 CDT)
- pair interaction cutoff Holly Freedman (Mon Aug 21 2006 - 21:51:30 CDT)
- NAMD2.6b2: Segmentation fault Morad Alawneh (Mon Aug 21 2006 - 12:00:47 CDT)
- Re: NAMD2.6b2: Segmentation fault Jim Phillips (Mon Aug 21 2006 - 15:05:37 CDT)
- why this error? Hamsa Priya Mohana sundaram (Mon Aug 21 2006 - 10:20:46 CDT)
- Lipids into NAMD Lechuga, Javier (Mon Aug 21 2006 - 06:10:30 CDT)
- Lipid into NAMD Lechuga, Javier (Sat Aug 19 2006 - 09:33:26 CDT)
- SMD of TFIIB jonas condes (Fri Aug 18 2006 - 14:40:46 CDT)
- small query... hl332_at_drexel.edu (Fri Aug 18 2006 - 11:17:25 CDT)
- bad global exclusion count in LES Dhiraj Srivastava (Fri Aug 18 2006 - 02:11:11 CDT)
- topology and parameter file for non aromatic nitrogen in ring system. Dhiraj Srivastava (Thu Aug 17 2006 - 22:15:57 CDT)
- Re: long range electrostatics for alchemical transformation nmichaud_at_jhu.edu (Thu Aug 17 2006 - 20:38:13 CDT)
- NAMD OSX Xgrid Matthew Wilce (Thu Aug 17 2006 - 19:45:58 CDT)
- NAMD 2.6b1 released Jim Phillips (Thu Aug 17 2006 - 18:24:22 CDT)
- alchemical transformation Michael A. Wilson (Thu Aug 17 2006 - 12:04:55 CDT)
- deprotonated form of Proline molecule Dhiraj Srivastava (Tue Aug 15 2006 - 14:55:35 CDT)
- n terminal patch on proline Dhiraj Srivastava (Tue Aug 15 2006 - 11:53:47 CDT)
- Pulling of Center of Mass Rahul Bhowmik (Tue Aug 15 2006 - 10:44:07 CDT)
- Building for SunGrid Jonathan D. Proulx (Tue Aug 15 2006 - 09:05:38 CDT)
- negatively charged proline as substrate Dhiraj Srivastava (Mon Aug 14 2006 - 11:08:40 CDT)
- CHARMM top and par files for PO4 Alexe Bojovschi (Mon Aug 14 2006 - 03:53:20 CDT)
- user defined restraints? Georgios Papadopoulos (Fri Aug 11 2006 - 04:41:17 CDT)
- Ion Channel Jarzynski Alessandro Cembran (Thu Aug 10 2006 - 17:56:29 CDT)
- where is PSUL? Heme cystein link question? youbin tu (Thu Aug 10 2006 - 11:01:50 CDT)
- Linking with -memory paranoid Cesar Luis Avila (Thu Aug 10 2006 - 10:49:43 CDT)
- 2D Ewald summation Xiongce Zhao (Thu Aug 10 2006 - 10:08:46 CDT)
- Changes to dihedral angles Neelanjana Sengupta (Wed Aug 09 2006 - 17:14:36 CDT)
- Running NAMD on debug mode Cesar Luis Avila (Wed Aug 09 2006 - 09:46:06 CDT)
- Fwd: extracting waters from DCD yi wang (Tue Aug 08 2006 - 16:50:55 CDT)
- Cham++ errors Kramer Campen (Tue Aug 08 2006 - 15:01:07 CDT)
- extracting waters from DCD Narender Singh Maan (Tue Aug 08 2006 - 14:04:04 CDT)
- data structure of neighbor list bqluan (Tue Aug 08 2006 - 10:37:52 CDT)
- questions regarding output data of an ABF simulation Anahita Tafvizi (Mon Aug 07 2006 - 15:27:34 CDT)
- Problem with Alchemical FEP Jawahar Neelankatan (Mon Aug 07 2006 - 09:24:55 CDT)
- atom type HZ4 not found Dhiraj Srivastava (Sat Aug 05 2006 - 13:27:12 CDT)
- pairinteractionSelf Holly Freedman (Thu Aug 03 2006 - 21:41:55 CDT)
- topology file with CT carbon Lacramioara Negureanu (Thu Aug 03 2006 - 19:46:59 CDT)
- Simulation of a 1000 water molecules Shenoy, Sukesh (Thu Aug 03 2006 - 13:19:34 CDT)
- Re: Simulation of a 1000 water molecules L. Michel Espinoza-Fonseca (Thu Aug 03 2006 - 14:34:47 CDT)
- Re: Simulation of a 1000 water molecules griadi_at_utalca.cl (Thu Aug 03 2006 - 15:12:37 CDT)
- Re: Simulation of a 1000 water molecules Brian Bennion (Thu Aug 03 2006 - 15:05:16 CDT)
- Re: Simulation of a 1000 water molecules Neelanjana Sengupta (Thu Aug 03 2006 - 15:11:37 CDT)
- Re: Simulation of a 1000 water molecules Jerome Henin (Thu Aug 03 2006 - 16:35:29 CDT)
- fad topology and parameter file Dhiraj Srivastava (Thu Aug 03 2006 - 02:11:45 CDT)
- FEP implementation in NAMD nmichaud_at_jhu.edu (Wed Aug 02 2006 - 18:17:53 CDT)
- Using LES with AMBER parm files Kramer Campen (Wed Aug 02 2006 - 14:35:05 CDT)
- coordination chemistry with NAMD Gaurav Sharma (Wed Aug 02 2006 - 14:04:04 CDT)
- two chain in pdb file Dhiraj Srivastava (Tue Aug 01 2006 - 01:46:01 CDT)
- missing atoms in pdb file. Dhiraj Srivastava (Tue Aug 01 2006 - 01:36:04 CDT)
- Cell membranes with lipids different from POPC and POPE Lechuga, Javier (Mon Jul 31 2006 - 18:03:59 CDT)
- TeraGrid Efficiency a-yermakova_at_northwestern.edu (Mon Jul 31 2006 - 12:22:41 CDT)
- collision correction of Locally Enhanced Sampling Dhiraj Srivastava (Sun Jul 30 2006 - 15:14:52 CDT)
- Re: RDF.tcl griadi_at_utalca.cl (Fri Jul 28 2006 - 17:01:24 CDT)
- New alchemical FEP tutorial Jerome Henin (Fri Jul 28 2006 - 14:13:40 CDT)
- Alchemical Free Energy Perturbation Simulation Jawahar Neelankatan (Fri Jul 28 2006 - 11:18:20 CDT)
- simple query.. hl332_at_drexel.edu (Thu Jul 27 2006 - 11:06:39 CDT)
- About pressureProfile command for non-equilibrium system. Boyang Wang (Wed Jul 26 2006 - 19:50:20 CDT)
- Equilibration problem pedro mansilla (Wed Jul 26 2006 - 13:47:44 CDT)
- topology files a-yermakova_at_northwestern.edu (Wed Jul 26 2006 - 12:54:21 CDT)
- namdenergy Luca Bellucci (Wed Jul 26 2006 - 10:02:58 CDT)
- simulation crashing with nan Jackie (Wed Jul 26 2006 - 08:49:56 CDT)
- VDW energy in CHARMM force field Gan, Yong (Tue Jul 25 2006 - 15:49:37 CDT)
- NBFix and NAMD Neelanjana Sengupta (Tue Jul 25 2006 - 13:53:48 CDT)
- LES Jackie (Tue Jul 25 2006 - 11:54:51 CDT)
- psfgen gets ATP chiral atoms wrong John Wise (Mon Jul 24 2006 - 15:43:23 CDT)
- InfiniPath and NAMD David Sept (Mon Jul 24 2006 - 14:57:03 CDT)
- temp autocorrelation Swarna Patra (Sun Jul 23 2006 - 20:00:09 CDT)
- Torque aplication with SMD pedro mansilla (Sun Jul 23 2006 - 11:38:44 CDT)
- Queries on patches, GDP-topology gamini_at_ncbs.res.in (Sat Jul 22 2006 - 07:36:15 CDT)
- Autopsf a-yermakova_at_northwestern.edu (Fri Jul 21 2006 - 16:00:41 CDT)
- PME grid error during minimization a-yermakova_at_northwestern.edu (Fri Jul 21 2006 - 15:05:10 CDT)
- (No subject) a-yermakova_at_northwestern.edu (Fri Jul 21 2006 - 15:04:47 CDT)
- unit cell information from dcd file Hamsa Priya Mohana sundaram (Thu Jul 20 2006 - 11:34:51 CDT)
- Tcl parsing of NAMD config file does not work. Klon, Anthony (Thu Jul 20 2006 - 07:43:09 CDT)
- need pair interaction energies, not forces Holly Freedman (Wed Jul 19 2006 - 22:20:06 CDT)
- #QNAN: Please help! a-yermakova_at_northwestern.edu (Wed Jul 19 2006 - 14:09:40 CDT)
- total mol calculation Jackie (Wed Jul 19 2006 - 14:08:07 CDT)
- total mol calculation Jackie (Wed Jul 19 2006 - 14:07:57 CDT)
- bulid psf for structure already with hydrogens Ching Wong (Wed Jul 19 2006 - 14:02:32 CDT)
- Re: About the unit of "efield" a-yermakova_at_northwestern.edu (Wed Jul 19 2006 - 13:24:39 CDT)
- help!!! hl332_at_drexel.edu (Wed Jul 19 2006 - 00:12:23 CDT)
- plz help!! hl332_at_drexel.edu (Tue Jul 18 2006 - 10:30:07 CDT)
- About the unit of "efield" wang (Tue Jul 18 2006 - 00:28:03 CDT)
- FATAL ERROR: pairlist i_upper mismatch! xiaojing gong (Mon Jul 17 2006 - 21:43:46 CDT)
- Minimizing and Equilibrating a-yermakova_at_northwestern.edu (Mon Jul 17 2006 - 13:12:52 CDT)
- linux cluster problems Per Jr. Greisen (Mon Jul 17 2006 - 04:20:57 CDT)
- Restarting velocities Per Jr. Greisen (Sun Jul 16 2006 - 05:47:58 CDT)
- unsubscribe Raj NK (Sat Jul 15 2006 - 21:46:00 CDT)
- Possible bug on NAMD 2.6B1? Cesar Avila (Sat Jul 15 2006 - 11:06:23 CDT)
- linux cluster problems Per Jr. Greisen (Sat Jul 15 2006 - 05:44:28 CDT)
- restart the simulation Tamal Banerjee (Fri Jul 14 2006 - 23:06:25 CDT)
- If I run NAMD on small computer, which processor is the best for NAMD under Linux? xiaojing gong (Fri Jul 14 2006 - 02:25:48 CDT)
- qsub on a linux cluster Per Jr. Greisen (Fri Jul 14 2006 - 02:12:54 CDT)
- splitting up long run leads to very different DNA conformation in E field Todd Trimble (Thu Jul 13 2006 - 18:40:10 CDT)
- log File - pressure not read a-yermakova_at_northwestern.edu (Thu Jul 13 2006 - 15:32:37 CDT)
- any SD minimization in NAMD? Ching Wong (Thu Jul 13 2006 - 14:59:57 CDT)
- NAMD on TeraGrid: OpenMP? a-yermakova_at_northwestern.edu (Thu Jul 13 2006 - 12:43:53 CDT)
- solvating a protein a-yermakova_at_northwestern.edu (Thu Jul 13 2006 - 11:16:04 CDT)
- NAMD on TeraGrid a-yermakova_at_northwestern.edu (Thu Jul 13 2006 - 11:04:17 CDT)
- About the module of "External Electric Field " wang (Wed Jul 12 2006 - 01:47:29 CDT)
- third time..can someone help!! hl332_at_drexel.edu (Tue Jul 11 2006 - 22:09:22 CDT)
- Computing Potential of Mean Force --SMD-cv gamini_at_ncbs.res.in (Tue Jul 11 2006 - 15:36:45 CDT)
- force calculation during to conformational change Gaurav Sharma (Tue Jul 11 2006 - 11:38:15 CDT)
- NVT nose-hoover hamiltonian in SMD? interesting.contraceptive_at_gmail.com (Mon Jul 10 2006 - 19:30:56 CDT)
- UseConstantRatio between "run" Alessandro Cembran (Mon Jul 10 2006 - 18:37:38 CDT)
- many short runs or one long run? Ching Wong (Mon Jul 10 2006 - 15:04:42 CDT)
- Protonation state Ching Wong (Mon Jul 10 2006 - 14:49:57 CDT)
- (No subject) a-yermakova_at_northwestern.edu (Mon Jul 10 2006 - 12:50:19 CDT)
- caps AYTUG TUNCEL (Mon Jul 10 2006 - 12:53:23 CDT)
- autoionize plugin.. hl332_at_drexel.edu (Mon Jul 10 2006 - 11:32:18 CDT)
- namdenergy plugin Chandra Ramananjara (Sun Jul 09 2006 - 23:47:10 CDT)
- RNA to DNA nisha_at_ncbs.res.in (Sat Jul 08 2006 - 00:29:24 CDT)
- across the nodes, namd jobs don't get enough CPU! M. Madhu (Fri Jul 07 2006 - 11:00:59 CDT)
- TCL Forces and Help on Script Joshua D. Moore (Thu Jul 06 2006 - 13:52:00 CDT)
- Rattle Algorithm Tamal Banerjee (Thu Jul 06 2006 - 01:52:49 CDT)
- Re: About the error of "Tcl interface" wang (Thu Jul 06 2006 - 00:26:31 CDT)
- About the error of "Tcl interface" wang (Wed Jul 05 2006 - 21:05:27 CDT)
- NAMD to Amber AYTUG TUNCEL (Tue Jul 04 2006 - 18:56:23 CDT)
- unsubscribe Noah Edelson (Tue Jul 04 2006 - 15:12:53 CDT)
- NAMDenergy Holly Freedman (Tue Jul 04 2006 - 12:44:59 CDT)
- OXT in pdb file nisha_at_ncbs.res.in (Tue Jul 04 2006 - 05:09:51 CDT)
- The problem of "SMD and smd.tcl" James W (Mon Jul 03 2006 - 20:33:57 CDT)
- Box size santanu chatterjee (Mon Jul 03 2006 - 16:33:33 CDT)
- Help on mutation Pijush Ghosh (Sun Jul 02 2006 - 01:24:19 CDT)
- Simulation Hangs during minimization Cesar Luis Avila (Mon Jul 03 2006 - 15:20:38 CDT)
- Data from Output file Tamal Banerjee (Mon Jul 03 2006 - 03:01:48 CDT)
- Protonation states Ching Wong (Fri Jun 30 2006 - 19:04:32 CDT)
- Problem equilibrating with low pressure santanu chatterjee (Fri Jun 30 2006 - 16:31:55 CDT)
- Constant Energy Simulations Eric Perim (Fri Jun 30 2006 - 08:42:48 CDT)
- Hi Moumita Maiti (Fri Jun 30 2006 - 04:26:18 CDT)
- what does "syntax error" mean in VMD? and does confinment to some residue will cause error? xiaojing gong (Thu Jun 29 2006 - 23:56:51 CDT)
- RE£º Re: £º Re: problems for runing NAMD on parallel computers xiaojing gong (Thu Jun 29 2006 - 23:32:46 CDT)
- Do I need to use an xsc file to restart a simulation in NVT? Ana Celia Araujo Vila Verde (Wed Jun 28 2006 - 10:41:07 CDT)
- Heating Up a system. Cesar Luis Avila (Thu Jun 29 2006 - 16:06:21 CDT)
- Do I need to use an xsc file to restart a simulation in NVT? Ana Celia Araujo Vila Verde (Wed Jun 28 2006 - 14:05:27 CDT)
- Binary for MacOSX-i686 Mikolai Fajer (Wed Jun 28 2006 - 13:53:00 CDT)
- Pressure control santanu chatterjee (Wed Jun 28 2006 - 13:43:52 CDT)
- problems for runing NAMD on parallel computers xiaojing gong (Wed Jun 28 2006 - 09:15:44 CDT)
- Problem with C++ libraries Baudilio Tejerina (Tue Jun 27 2006 - 10:29:32 CDT)
- psfgen and charmm19: is there any inconsistency? Magali Cottevieille (Tue Jun 27 2006 - 03:18:20 CDT)
- Calculating or Outputing Forces Joshua D. Moore (Mon Jun 26 2006 - 21:00:44 CDT)
- Time of MD edu (Fri Jun 23 2006 - 13:59:54 CDT)
- Question about Van der Waals radii Chandra Ramananjara (Mon Jun 26 2006 - 09:14:10 CDT)
- PME pair interaction analysis Holly Freedman (Sun Jun 25 2006 - 16:17:41 CDT)
- Re: Boiling temperature of water. Boyang Wang (Thu Jun 22 2006 - 21:38:54 CDT)
- Boiling temperature of water. Boyang Wang (Thu Jun 22 2006 - 19:20:09 CDT)
- Autoionize error: spontaneously quits dora guzman (Wed Jun 21 2006 - 18:38:51 CDT)
- Re: NAMD results depend on # of processors!!?? Jan Saam (Wed Jun 21 2006 - 16:25:21 CDT)
- calculation (continue) edu (Wed Jun 21 2006 - 16:03:40 CDT)
- error using Namdenergy Chandra Ramananjara (Wed Jun 21 2006 - 15:04:19 CDT)
- NAMD: run problem bo baker (Wed Jun 21 2006 - 14:53:41 CDT)
- Is clock skew a problem for charm++ Jan Saam (Tue Jun 20 2006 - 17:37:19 CDT)
- Re: Is clock skew a problem for charm++ Jan Saam (Tue Jun 20 2006 - 17:50:46 CDT)
- Re: Re: Is clock skew a problem for charm++ Gengbin Zheng (Wed Jun 21 2006 - 02:08:08 CDT)
- Re: Re: Is clock skew a problem for charm++ Jan Saam (Wed Jun 21 2006 - 08:52:54 CDT)
- Re: Re: Is clock skew a problem for charm++ Jan Saam (Wed Jun 21 2006 - 14:38:09 CDT)
- Re: Re: Is clock skew a problem for charm++ Gengbin Zheng (Wed Jun 21 2006 - 23:17:07 CDT)
- Re: Re: Is clock skew a problem for charm++ Jan Saam (Thu Jun 22 2006 - 06:56:26 CDT)
- Re: Re: Is clock skew a problem for charm++ Sameer Kumar (Thu Jun 22 2006 - 08:04:11 CDT)
- Re: Re: Is clock skew a problem for charm++ Jan Saam (Thu Jun 22 2006 - 12:54:47 CDT)
- NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) Jan Saam (Wed Jun 21 2006 - 15:55:13 CDT)
- Re: NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) Brian Bennion (Wed Jun 21 2006 - 17:24:11 CDT)
- Re: NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) Jan Saam (Thu Jun 22 2006 - 06:36:50 CDT)
- Re: NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) Jerome Henin (Wed Jun 21 2006 - 17:34:23 CDT)
- Re: NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) Jan Saam (Thu Jun 22 2006 - 06:45:47 CDT)
- Re: Re: Is clock skew a problem for charm++ hrh (Wed Jun 21 2006 - 06:33:05 CDT)
- Re: Re: Is clock skew a problem for charm++ Gengbin Zheng (Wed Jun 21 2006 - 02:08:08 CDT)
- Re: Is clock skew a problem for charm++ Jan Saam (Tue Jun 20 2006 - 17:50:46 CDT)
- Conversion for forces Gianluca Interlandi (Tue Jun 20 2006 - 14:05:28 CDT)
- Tcl, minimization and MD (Warning: I am a lazy ignorant) Edelmiro Moman (Tue Jun 20 2006 - 10:20:09 CDT)
- RE: Tcl, minimization and MD (Warning: I am a lazy ignorant) JC Gumbart (Tue Jun 20 2006 - 10:38:17 CDT)
- Re: Tcl, minimization and MD (Warning: I am a lazy ignorant) Peter Freddolino (Tue Jun 20 2006 - 10:40:52 CDT)
- Regarding box-size Moumita Maiti (Tue Jun 20 2006 - 06:32:43 CDT)
- Angle 2, Where is the problem [IMPORTANT] linefinc (Mon Jun 19 2006 - 11:50:41 CDT)
- support TIP5? doubt on high temperature MD Ching Wong (Mon Jun 19 2006 - 20:31:52 CDT)
- extended system or Basis Vector Ching Wong (Mon Jun 19 2006 - 20:29:01 CDT)
- non-cubic boxes for Periodic Boundary Conditions George M. Giambasu (Mon Jun 19 2006 - 17:38:31 CDT)
- Lipid bilayer center go away from center of system. ghg_at_xalt.am (Sun Jun 18 2006 - 10:10:38 CDT)
- chage free energy edu (Fri Jun 16 2006 - 13:58:08 CDT)
- Re. Namd window network problem edu (Fri Jun 16 2006 - 10:33:25 CDT)
- Angle CO2 Problem linefinc (Fri Jun 16 2006 - 06:08:23 CDT)
- Re: free energy calculate Taeho Kim (Fri Jun 16 2006 - 01:30:29 CDT)
- free energy calculate Taeho Kim (Fri Jun 16 2006 - 00:52:16 CDT)
- Vibrational mode analysis Gianluca Interlandi (Thu Jun 15 2006 - 19:31:40 CDT)
- Re: Vibrational mode analysis L. Michel Espinoza-Fonseca (Thu Jun 15 2006 - 19:47:29 CDT)
- Re: Vibrational mode analysis Michael Grabe (Thu Jun 15 2006 - 20:36:16 CDT)
- Re: Vibrational mode analysis Richard Law (Thu Jun 15 2006 - 20:52:18 CDT)
- NAMD: compile problem bo baker (Thu Jun 15 2006 - 19:04:58 CDT)
- problem in minimization while running Moumita Maiti (Thu Jun 15 2006 - 15:59:50 CDT)
- NAMD compile in Mac OSX and IBM XL C/C++ bo baker (Thu Jun 15 2006 - 15:18:56 CDT)
- psfgen: last CTER does not work Morad Alawneh (Thu Jun 15 2006 - 14:30:14 CDT)
- Namd window network problem edu (Thu Jun 15 2006 - 13:55:51 CDT)
- help with adding a new force filed into NAMD liu liuxiandong (Thu Jun 15 2006 - 10:44:10 CDT)
- slow NAMD simulations on a AMD athlon64 in SUSE linux Fam Eklund (Wed Jun 14 2006 - 16:28:38 CDT)
- Compile NAMD on Bluegene Dong Luo (Wed Jun 14 2006 - 16:17:13 CDT)
- Re: Compile NAMD on Bluegene Mgr. Lubos Vrbka (Thu Jun 15 2006 - 01:01:25 CDT)
- Re: Compile NAMD on Bluegene Gengbin Zheng (Thu Jun 15 2006 - 01:11:34 CDT)
- Re: Compile NAMD on Bluegene Dong Luo (Thu Jun 15 2006 - 09:48:32 CDT)
- Re: Compile NAMD on Bluegene Gengbin Zheng (Thu Jun 15 2006 - 12:16:40 CDT)
- Re: Compile NAMD on Bluegene Dong Luo (Thu Jun 15 2006 - 14:16:30 CDT)
- Re: Compile NAMD on Bluegene Dong Luo (Fri Jun 16 2006 - 13:56:46 CDT)
- Re: Compile NAMD on Bluegene Dong Luo (Thu Jun 15 2006 - 11:35:18 CDT)
- Re: Compile NAMD on Bluegene Gengbin Zheng (Thu Jun 15 2006 - 12:04:49 CDT)
- Re: Compile NAMD on Bluegene Gengbin Zheng (Thu Jun 15 2006 - 01:11:34 CDT)
- Re: Compile NAMD on Bluegene Mgr. Lubos Vrbka (Thu Jun 15 2006 - 01:01:25 CDT)
- namd: problem bo baker (Wed Jun 14 2006 - 12:04:47 CDT)
- Superctitiacal CO2 linefinc (Wed Jun 14 2006 - 09:58:58 CDT)
- the patching problem in psfgen Moumita Maiti (Wed Jun 14 2006 - 06:13:20 CDT)
- Altix performances Alessandro Cembran (Tue Jun 13 2006 - 17:40:59 CDT)
- Velocity unit ofvelocity in NAMD the binary files Amin R. Mazloom (Tue Jun 13 2006 - 15:43:09 CDT)
- namd: problem bo baker (Tue Jun 13 2006 - 14:16:56 CDT)
- Unit of Velocity in the Velocity files Amin R. Mazloom (Tue Jun 13 2006 - 11:36:56 CDT)
- Is the GBSA model in NAMD ? wang (Tue Jun 13 2006 - 01:42:14 CDT)
- Re: Is the GBSA model in NAMD ? Mark Abraham (Tue Jun 13 2006 - 02:00:01 CDT)
- Re: Is the GBSA model in NAMD ? wang (Tue Jun 13 2006 - 04:03:08 CDT)
- Re: Is the GBSA model in NAMD ? Joshua D. Moore (Tue Jun 13 2006 - 12:32:49 CDT)
- Re: Is the GBSA model in NAMD ? dimka (Tue Jun 13 2006 - 15:17:55 CDT)
- Re: Is the GBSA model in NAMD ? Mark Abraham (Tue Jun 13 2006 - 22:24:30 CDT)
- Re: Is the GBSA model in NAMD ? Richard Wood (Wed Jun 14 2006 - 05:22:22 CDT)
- Re: Is the GBSA model in NAMD ? Mark Abraham (Wed Jun 14 2006 - 09:00:45 CDT)
- Re: Is the GBSA model in NAMD ? Peter Freddolino (Wed Jun 14 2006 - 09:16:58 CDT)
- Re: Is the GBSA model in NAMD ? Mark Abraham (Tue Jun 13 2006 - 02:00:01 CDT)
- (no subject) Michael Grabe (Mon Jun 12 2006 - 20:38:48 CDT)
- setenv: command not found bo baker (Mon Jun 12 2006 - 18:55:39 CDT)
- Pairlist warnings Alessandro Cembran (Sat Jun 10 2006 - 16:58:07 CDT)
- Interrupted system call Edelmiro Moman (Fri Jun 09 2006 - 02:21:25 CDT)
- question on phosphotyrosine parameters from charmm Mao Xiang (Thu Jun 08 2006 - 22:32:06 CDT)
- Re: Some problem on pair force calculation Sting (Thu Jun 08 2006 - 20:40:11 CDT)
- DCD to PDB conversion Edelmiro Moman (Thu Jun 08 2006 - 02:57:31 CDT)
- Constant electric field to selected atoms. hamdi (Wed Jun 07 2006 - 09:08:32 CDT)
- Factorization in PMEGridSize Edelmiro Moman (Wed Jun 07 2006 - 04:36:54 CDT)
- Where to put the "nodelist" file Edelmiro Moman (Wed Jun 07 2006 - 02:45:37 CDT)
- Some problem on pair force calculation Sting (Tue Jun 06 2006 - 22:27:30 CDT)
- TCL forces and boundary conditions Tyler Luchko (Tue Jun 06 2006 - 18:23:27 CDT)
- Re: vmd-l: snoze pa (Tue Jun 06 2006 - 17:47:34 CDT)
- output on Linux-amd64-MPI Seungho Choe (Tue Jun 06 2006 - 15:47:33 CDT)
- Some problem on pair force calculation Sting (Tue Jun 06 2006 - 08:32:48 CDT)
- PMF error wang (Mon Jun 05 2006 - 21:38:18 CDT)
- a error during install charm-5.9 snowyowls (Mon Jun 05 2006 - 18:45:14 CDT)
- CMAP and NAMD L. Michel Espinoza-Fonseca (Mon Jun 05 2006 - 19:16:21 CDT)
- getting #.IND #QNAN after phase 8 Amin R. Mazloom (Mon Jun 05 2006 - 14:25:25 CDT)
- FEP error "atoms moving too fast" jz7_at_duke.edu (Sun Jun 04 2006 - 10:39:37 CDT)
- the patch between segments for multiple chains molecule. Moumita Maiti (Fri Jun 02 2006 - 12:14:58 CDT)
- Error on renaming file Morad Alawneh (Fri Jun 02 2006 - 10:31:21 CDT)
- A puzzling problem about adsorption energy in solution. Boyang Wang (Thu Jun 01 2006 - 17:39:26 CDT)
- help on compiling error Binquan luan (Thu Jun 01 2006 - 11:32:44 CDT)
- Starting out with NAMD/VMD nisha_at_ncbs.res.in (Thu Jun 01 2006 - 02:22:21 CDT)
- Re: Re: Large energy fluctuation Sting (Tue May 31 2005 - 21:38:38 CDT)
- Free energy from MD Simulation Nitin Bhardwaj (Wed May 31 2006 - 17:13:51 CDT)
- Large energy fluctuation Sting (Mon May 30 2005 - 21:44:44 CDT)
- Density of water santanu chatterjee (Tue May 30 2006 - 14:04:32 CDT)
- parallel NAMD output problem ARTURAS ZIEMYS (Tue May 30 2006 - 11:27:36 CDT)
- Re: ABF: example works; more questions. Jan Saam (Tue May 30 2006 - 11:01:29 CDT)
- SMD Energy Pijush Ghosh (Tue May 30 2006 - 10:47:32 CDT)
- Repeating again: Periodic velocity pulls hl332_at_drexel.edu (Tue May 30 2006 - 09:51:14 CDT)
- ABF: example works now; more questions. Jan Saam (Tue May 30 2006 - 08:57:15 CDT)
- Large energy fluctuation Sting (Fri Apr 08 2005 - 07:09:07 CDT)
- FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CAI Per Jr. Greisen (Tue May 30 2006 - 04:08:56 CDT)
- questions regrading ABF Jan Saam (Mon May 29 2006 - 10:47:48 CDT)
- [Fwd: Re: Specific Heat Calculation with VMD] Ayþe Özlem Sezerman (Mon May 29 2006 - 08:31:31 CDT)
- Basic question about steered moledular dynamic(SMD) simulation q=E2=BA=E9=C3=F7?= (Mon May 29 2006 - 00:49:42 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation JC Gumbart (Mon May 29 2006 - 00:36:34 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation q=90=B4=E6=B4=AA=E6=98=8E?= (Mon May 29 2006 - 03:54:12 CDT)
- RE: Basic question about steered moledular dynamic(SMD) simulation JC Gumbart (Mon May 29 2006 - 09:51:02 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation q=E2=BA=E9=C3=F7?= (Tue May 30 2006 - 11:22:42 CDT)
- RE: Basic question about steered moledular dynamic(SMD) simulation JC Gumbart (Mon May 29 2006 - 12:01:21 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation q=E2=BA=E9=C3=F7?= (Wed May 31 2006 - 00:05:38 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation q=E2=BA=E9=C3=F7?= (Wed May 31 2006 - 03:48:41 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation JC Gumbart (Tue May 30 2006 - 11:47:58 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation q=90=B4=E6=B4=AA=E6=98=8E?= (Wed May 31 2006 - 01:45:20 CDT)
- RE: Basic question about steered moledular dynamic(SMD) simulation JC Gumbart (Wed May 31 2006 - 09:19:11 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation q=90=B4=E6=B4=AA=E6=98=8E?= (Mon May 29 2006 - 03:54:12 CDT)
- Re: Basic question about steered moledular dynamic(SMD) simulation JC Gumbart (Mon May 29 2006 - 00:36:34 CDT)
- Periodic cell has become too small santanu chatterjee (Sun May 28 2006 - 17:42:29 CDT)
- Basic question. Taeho Kim (Fri May 26 2006 - 20:24:54 CDT)
- Free energy with amber topology Stefano Corni (Fri May 26 2006 - 02:53:28 CDT)
- Periodic velcoity pulls hl332_at_drexel.edu (Fri May 26 2006 - 12:15:55 CDT)
- [Fwd: Specific Heat Calculation with VMD] Ayþe Özlem Sezerman (Fri May 26 2006 - 09:29:31 CDT)
- Specific Heat Calculation with VMD Ayþe Özlem Sezerman (Fri May 26 2006 - 08:46:02 CDT)
- Remove water to close to the protein? Per Jr. Greisen (Fri May 26 2006 - 07:59:27 CDT)
- Spike during minimization of protein with water Per Jr. Greisen (Fri May 26 2006 - 02:47:01 CDT)
- something about simulation of small molecules in NAMD q=CF=20=B3=C2?= (Thu May 25 2006 - 21:00:43 CDT)
- Water simulation with namd santanu chatterjee (Wed May 24 2006 - 16:32:49 CDT)
- How to make a virtual bond? patrick wintrode (Wed May 24 2006 - 13:27:24 CDT)
- Transition path sampling Hemant Kushwaha (Tue May 23 2006 - 09:11:17 CDT)
- Re: make the helix longer lily jin (Mon May 22 2006 - 15:19:57 CDT)
- make the helix longer lily jin (Mon May 22 2006 - 13:16:06 CDT)
- Saving the coordinates of DCD file in pdb format Ayþe Özlem Sezerman (Mon May 22 2006 - 04:50:45 CDT)
- About loadcoors -- is there a loadvelocity? Boyang Wang (Fri May 19 2006 - 13:01:11 CDT)
- NDON! and NACC! in Parameter Files Joshua D. Moore (Thu May 18 2006 - 19:10:28 CDT)
- DCD file Ayse Ozlem Sezerman (Thu May 18 2006 - 02:09:40 CDT)
- LDB problem on Dual Atlon64 X2 Sebastian Wasilewski (Wed May 17 2006 - 17:07:17 CDT)
- How to turn off electrostatic interactions (PME). Maxim Fedorov (Wed May 17 2006 - 15:58:07 CDT)
- Rigid bonds for United Atom Methylene Chloride CH2Cl2 Joshua D. Moore (Wed May 17 2006 - 15:22:41 CDT)
- pair interaction analysis of multiple trajectories with different timestep Shirley Li (Wed May 17 2006 - 10:18:03 CDT)
- question on the charged system Hyonseok Hwang (Wed May 17 2006 - 01:31:08 CDT)
- SMD lily jin (Tue May 16 2006 - 19:18:28 CDT)
- How to make a disulphide bond lily jin (Tue May 16 2006 - 13:02:51 CDT)
- Re: Simulation on AMD64 Dual Core - threads lose connection Sławek Orłowski (Tue May 16 2006 - 01:04:39 CDT)
- pair interaction Shirley Li (Mon May 15 2006 - 19:13:27 CDT)
- NAMD support for MNDO semi-empirical model Chandra Ramananjara (Mon May 15 2006 - 10:34:07 CDT)
- Cannot open file 'pair.pdb' Sandeep Agrawal (Mon May 15 2006 - 07:32:42 CDT)
- Taurine parameters Morad Alawneh (Sat May 13 2006 - 10:13:50 CDT)
- UNABLE TO OPEN XPLOR PARAMETER FILE alanin.params Sandeep Agrawal (Fri May 12 2006 - 04:17:06 CDT)
- Nose-Hoover langevin piston pressure control and target surface tension Hyonseok Hwang (Thu May 11 2006 - 23:04:55 CDT)
- Water liquid-vapor interface Jindal Shah (Thu May 11 2006 - 13:24:43 CDT)
- cluster / scratch space ziemys_at_ecr6.ohio-state.edu (Thu May 11 2006 - 09:28:06 CDT)
- How to include more parameterfiles in NAMD Per Jr. Greisen (Thu May 11 2006 - 09:36:36 CDT)
- Simulation on AMD64 Dual Core - threads lose connection Sławek Orłowski (Thu May 11 2006 - 02:42:00 CDT)
- explicit hydrogen bonds Matthew Wilce (Thu May 11 2006 - 00:54:20 CDT)
- namd: adding water molecules Sergio Anis (Wed May 10 2006 - 21:12:43 CDT)
- namd: adding water molecules Sergio Anis (Wed May 10 2006 - 21:52:33 CDT)
- CMAP Per Jr. Greisen (Wed May 10 2006 - 12:04:07 CDT)
- periodic cell too small genie lfs (Wed May 10 2006 - 04:48:44 CDT)
- Some basic questions about NAMD Shirley Li (Tue May 09 2006 - 15:01:37 CDT)
- les + conformational free energy L. Michel Espinoza-Fonseca (Tue May 09 2006 - 08:31:51 CDT)
- Re: Heme - Cysteine link Sławek Orłowski (Tue May 09 2006 - 08:20:50 CDT)
- CMAP Per Jr. Greisen (Tue May 09 2006 - 06:16:45 CDT)
- Heme - Cysteine link Muhittin Emre Özdemir (Tue May 09 2006 - 04:06:46 CDT)
- Re: About timestep again. Boyang Wang (Mon May 08 2006 - 17:38:07 CDT)
- About timestep again. -- Fastest motion O-H streching period 10 fs. Boyang Wang (Mon May 08 2006 - 11:14:37 CDT)
- Timestep -- Can I use 2 fs timestep for 50 nanoseconds simulation? Boyang Wang (Mon May 08 2006 - 10:22:05 CDT)
- Timestep. Boyang Wang (Mon May 08 2006 - 10:05:17 CDT)
- hi... Navratna Vajpai (Mon May 08 2006 - 04:36:33 CDT)
- change in Disulphide Patches Navratna Vajpai (Mon May 08 2006 - 03:05:28 CDT)
- Clustermatic and NFS mount Gianluca Interlandi (Sun May 07 2006 - 15:49:40 CDT)
- a basic question Tamal Banerjee (Sun May 07 2006 - 12:04:31 CDT)
- protein moves away from water box Shirley Li (Fri May 05 2006 - 14:25:40 CDT)
- sound velocity of water Binquan luan (Thu May 04 2006 - 18:10:53 CDT)
- Cannot specify both an initial temperature and a velocity file Osman Yogurtcu (Thu May 04 2006 - 06:44:03 CDT)
- MMPBSA... Raul Araya Secchi (Wed May 03 2006 - 16:23:46 CDT)
- Asymmetric water molecule found??? Elsa F. Sousa Henriques (Wed May 03 2006 - 02:59:26 CDT)
- TRIO Gianluca Interlandi (Tue May 02 2006 - 16:55:09 CDT)
- [Fwd: Re: SMD of small molecule dimer] dora guzman (Tue May 02 2006 - 11:59:32 CDT)
- convert .dcd into .trr Shirley Li (Tue May 02 2006 - 12:37:53 CDT)
- one residue rmsd snoze pa (Mon May 01 2006 - 17:49:02 CDT)
- fix atoms in minimisation Maria Gonzalez (Mon May 01 2006 - 10:14:35 CDT)
- about TCL boundary forces gbellesia_at_chem.ucsb.edu (Sat Apr 29 2006 - 17:16:54 CDT)
- parameters for camphor Sergio Anis (Mon May 01 2006 - 12:35:04 CDT)
- SMD of small molecule dimer dora guzman (Fri Apr 28 2006 - 12:05:39 CDT)
- SMD of small molecule dimer dora guzman (Thu Apr 27 2006 - 19:28:20 CDT)
- simulated annealing genie lfs (Mon May 01 2006 - 11:04:35 CDT)
- [Fwd: HD speed ??] Mark Abraham (Sun Apr 30 2006 - 12:28:04 CDT)
- HD speed ?? Georgios Papadopoulos (Sun Apr 30 2006 - 03:13:36 CDT)
- NAD splits up into 3 pieces Per Jr. Greisen (Sun Apr 30 2006 - 07:13:02 CDT)
- simulations of periodic lattice List User (Sun Apr 30 2006 - 02:38:00 CDT)
- Simulation with denaturants? patrick wintrode (Sat Apr 29 2006 - 14:00:02 CDT)
- how long should the simulation be run genie lfs (Sat Apr 29 2006 - 04:33:50 CDT)
- parameter and topology file for ethanol Per Jr. Greisen (Sat Apr 29 2006 - 03:32:42 CDT)
- Re: modeling zinc binding site Jan Kosinski (Fri Apr 28 2006 - 10:25:20 CDT)
- OPLS force field for carbon tetrachloride ( ccl4 ) ? wzhuang (Fri Apr 28 2006 - 02:15:44 CDT)
- why pressure is fluctuating so much Tamal Banerjee (Thu Apr 27 2006 - 22:40:28 CDT)
- error message snoze pa (Thu Apr 27 2006 - 16:15:35 CDT)
- binary.coor to ascII.coor paul.dalhaimer_at_yale.edu (Thu Apr 27 2006 - 12:14:52 CDT)
- how to add charged particles manually. ayhan duzgun (Wed Apr 26 2006 - 21:24:13 CDT)
- two references- I got them, thank you! Ioana Cozmuta (Wed Apr 26 2006 - 16:15:11 CDT)
- two references Ioana Cozmuta (Wed Apr 26 2006 - 15:18:28 CDT)
- NAMD is unstable on myrinet connecting cpus xiaojing gong (Wed Apr 26 2006 - 09:15:21 CDT)
- How to deal with a long path in ABF simulation? Wenyu Zhong (Wed Apr 26 2006 - 09:34:31 CDT)
- question on pulling direction lzshen (Wed Apr 26 2006 - 11:41:46 CDT)
- scaling NAMD2.6B1 on IBM P5 Thomas C. Bishop (Tue Apr 25 2006 - 14:44:33 CDT)
- still on tcl boundary forces gbellesia_at_chem.ucsb.edu (Tue Apr 25 2006 - 12:34:52 CDT)
- smd dimer dissociation L. Michel Espinoza-Fonseca (Tue Apr 25 2006 - 11:24:12 CDT)
- part of a protein AYTUG TUNCEL (Tue Apr 25 2006 - 02:58:42 CDT)
- error related to tcl boundary forces gbellesia_at_chem.ucsb.edu (Tue Apr 25 2006 - 00:52:38 CDT)
- modeling zinc binding site Jan Kosinski (Tue Apr 25 2006 - 07:46:30 CDT)
- parameter and topology for cyclodextrin! Íõº£Ãû (Mon Apr 24 2006 - 23:58:57 CDT)
- NAMD configuration files for NVT ensemble Lechuga, Javier (Sat Apr 22 2006 - 12:15:08 CDT)
- simulated annealing with explicit water L. Michel Espinoza-Fonseca (Mon Apr 24 2006 - 05:37:30 CDT)
- Faltal Error. reassignFreq fails Martin Loewer (Fri Apr 21 2006 - 05:50:28 CDT)
- Re: Re: water hole Sting (Thu Apr 20 2006 - 22:15:42 CDT)
- Re: Re: water hole Sting (Sat Apr 20 2002 - 21:28:49 CDT)
- water hole Sting (Fri Apr 19 2002 - 21:45:40 CDT)
- RE: Computing cost of frozen atoms Jacob Pøhlsgaard (Wed Apr 19 2006 - 03:33:28 CDT)
- namd2 on IBM P5 hangs Rene Salmon (Wed Apr 19 2006 - 13:34:16 CDT)
- custom pulling path Raul Alcantara (Wed Apr 19 2006 - 12:30:13 CDT)
- different cutoff for elecstrostatic and VDW interactions Hyonseok Hwang (Tue Apr 18 2006 - 12:53:29 CDT)
- Computing cost of frozen atoms Jacob Pøhlsgaard (Tue Apr 18 2006 - 04:39:20 CDT)
- Multiplicity of parameters Rahul Bhowmik (Tue Apr 18 2006 - 09:36:22 CDT)
- Clustering of conformation Leo.Ghemtio_at_sanofi-aventis.com (Tue Apr 18 2006 - 04:25:02 CDT)
- How to deal with this sugar residues though psfgen? q=E2=BA=E9=C3=F7?= (Tue Apr 18 2006 - 00:51:58 CDT)
- amidated C-terminus (NH2) with OPLS force field Giovanni Bellesia (Mon Apr 17 2006 - 17:34:57 CDT)
- OPLS-AA/L Giovanni Bellesia (Mon Apr 17 2006 - 15:53:34 CDT)
- MD analysis snoze pa (Mon Apr 17 2006 - 14:37:31 CDT)
- FEP, IONS, DUMMY atoms, LARGE numbers Raul Araya Secchi (Mon Apr 17 2006 - 12:32:55 CDT)
- About the command "set z [lindex $coorList($i) 2]". Boyang Wang (Sat Apr 15 2006 - 19:47:04 CDT)
- Re: vmd-l: breaking the DCD file snoze pa (Sun Apr 16 2006 - 17:08:31 CDT)
- Multiple residues at same position snoze pa (Sun Apr 16 2006 - 02:01:35 CDT)
- question about protein leaving water box TZU-LAN YEH (Fri Apr 14 2006 - 21:05:17 CDT)
- tcl boundary forces Giovanni Bellesia (Fri Apr 14 2006 - 13:26:16 CDT)
- vmd-l: Generating PSF for 1JNO.pdb chain A Lin (Fri Apr 14 2006 - 10:29:07 CDT)
- Periodic cell has become too small for original patch grid! lily jin (Thu Apr 13 2006 - 11:40:24 CDT)
- High VDW energies during minimization and dynamics Deva Priyakumar (Thu Apr 13 2006 - 10:23:38 CDT)
- RE: High VDW energies during minimization and dynamics Pijush Ghosh (Thu Apr 13 2006 - 11:52:35 CDT)
- Re: High VDW energies during minimization and dynamics Brian Bennion (Thu Apr 13 2006 - 12:47:30 CDT)
- Re: High VDW energies during minimization and dynamics Peter Freddolino (Thu Apr 13 2006 - 13:22:07 CDT)
- NAMD-L: question about SMDk, the force constant for SMD Margaret Shun Cheung (Wed Apr 12 2006 - 23:27:27 CDT)
- ACE patch paul.dalhaimer_at_yale.edu (Wed Apr 12 2006 - 10:56:46 CDT)
- reconstructing PMF Ioana Cozmuta (Tue Apr 11 2006 - 16:57:02 CDT)
- help on NAMD code Binquan luan (Tue Apr 11 2006 - 13:12:12 CDT)
- General question about psfgen atoms. snoze pa (Tue Apr 11 2006 - 12:27:27 CDT)
- namd + opteron/xeon L. Michel Espinoza-Fonseca (Mon Apr 10 2006 - 11:55:56 CDT)
- Developing topologies for modified NA residues? Jacob Pøhlsgaard (Mon Apr 10 2006 - 08:37:04 CDT)
- About restart.vel.old file. Boyang Wang (Fri Apr 07 2006 - 22:15:58 CDT)
- error about tclForcesScript xiaojing gong (Mon Apr 10 2006 - 09:21:13 CDT)
- How to measure of radius of a molecules? Taeho Kim (Mon Apr 10 2006 - 03:30:28 CDT)
- Constrain only in Z direction xiaojing gong (Sun Apr 09 2006 - 22:32:02 CDT)
- Multimeric protein Gianluca Interlandi (Sat Apr 08 2006 - 16:57:28 CDT)
- system calls inside namd script Himanshu Khandelia (Sat Apr 08 2006 - 16:42:46 CDT)
- NAMD-L: question about harmonic constraints Margaret Shun Cheung (Sat Apr 08 2006 - 13:33:33 CDT)
- RE: NAMD-L: question about harmonic constraints JC Gumbart (Sat Apr 08 2006 - 13:52:02 CDT)
- RE: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Sat Apr 08 2006 - 22:30:13 CDT)
- RE: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Mon Apr 10 2006 - 09:52:05 CDT)
- RE: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Mon Apr 10 2006 - 12:54:57 CDT)
- Re: NAMD-L: question about harmonic constraints JC Gumbart (Mon Apr 10 2006 - 17:50:58 CDT)
- Re: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Mon Apr 10 2006 - 18:26:27 CDT)
- Re: NAMD-L: question about harmonic constraints JC Gumbart (Tue Apr 11 2006 - 17:41:08 CDT)
- Re: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Tue Apr 11 2006 - 21:06:33 CDT)
- RE: NAMD-L: question about harmonic constraints JC Gumbart (Tue Apr 11 2006 - 23:43:40 CDT)
- RE: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Wed Apr 12 2006 - 11:25:23 CDT)
- RE: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Wed Apr 12 2006 - 13:31:20 CDT)
- RE: NAMD-L: question about harmonic constraints Gianluca Interlandi (Wed Apr 12 2006 - 17:05:24 CDT)
- RE: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Wed Apr 12 2006 - 17:29:50 CDT)
- RE: NAMD-L: question about harmonic constraints Margaret Shun Cheung (Wed Apr 12 2006 - 22:05:14 CDT)
- RE: NAMD-L: question about harmonic constraints JC Gumbart (Sat Apr 08 2006 - 13:52:02 CDT)
- A strange phenomenon in my dynamics system,any suggestion? ËïÍ¥¹ã (Fri Apr 07 2006 - 21:29:32 CDT)
- How to patch residues in different chains snoze pa (Fri Apr 07 2006 - 18:32:38 CDT)
- difference between reassignfreq and rescalefreq in temperature controls. Margaret Shun Cheung (Fri Apr 07 2006 - 13:13:16 CDT)
- a name quesiton lily jin (Fri Apr 07 2006 - 11:19:41 CDT)
- parameter file for DAD Yu Wang (Fri Apr 07 2006 - 09:18:55 CDT)
- RE: Bizarre atom behavior Chang, Christopher (Thu Apr 06 2006 - 16:40:04 CDT)
- Re: vmd-l:namd-l; question about psfgen (param for CT1?) Margaret Shun Cheung (Thu Apr 06 2006 - 15:53:20 CDT)
- Re: vmd-l: dummy atoms and FEP Peter Freddolino (Thu Apr 06 2006 - 11:45:26 CDT)
- dummy atoms and FEP Raul Araya Secchi (Thu Apr 06 2006 - 11:36:57 CDT)
- tcouple vs langevin Margaret Shun Cheung (Thu Apr 06 2006 - 10:53:46 CDT)
- residue name and segment name Tamal Banerjee (Thu Apr 06 2006 - 02:05:07 CDT)
- Bizarre atom behavior Chang, Christopher (Wed Apr 05 2006 - 11:35:54 CDT)
- Problem about the energy change of refold of SMD protein TCWu (Wed Apr 05 2006 - 18:53:35 CDT)
- CMAP in NAMD? mpavlova_at_purdue.edu (Wed Apr 05 2006 - 16:34:58 CDT)
- running NAMD on beowulf cluster Nitin Bhardwaj (Wed Apr 05 2006 - 14:17:31 CDT)
- minimize in FEP.... Raul Araya (Wed Apr 05 2006 - 10:55:56 CDT)
- A possibel wrong coding in Parameters::read_charmm_parameter_file(char *) Qikai Li (Wed Apr 05 2006 - 10:25:56 CDT)
- NAMD-L:density of water molecules in a water sphere Margaret Shun Cheung (Tue Apr 04 2006 - 12:08:01 CDT)
- Tpr Ching Wong (Tue Apr 04 2006 - 10:55:33 CDT)
- help on error message during compiling Binquan luan (Mon Apr 03 2006 - 19:43:14 CDT)
- other crystal types in NAMD ? Himanshu Khandelia (Tue Apr 04 2006 - 10:17:40 CDT)
- Energy due to electric field jcm203_at_soton.ac.uk (Tue Apr 04 2006 - 09:09:18 CDT)
- langevinHydrogen off? Gianluca Interlandi (Mon Apr 03 2006 - 18:15:23 CDT)
- density of water molecules in a water sphere Margaret Shun Cheung (Mon Apr 03 2006 - 13:56:42 CDT)
- restart a simulation lily jin (Mon Apr 03 2006 - 12:25:57 CDT)
- PMEGridSize Anuradha Mittal (Sun Apr 02 2006 - 21:18:38 CDT)
- math formula for spherical boundary conditions. Margaret Shun Cheung (Sun Apr 02 2006 - 15:44:11 CDT)
- questions about the use of HIS residue xiaojing gong (Sun Apr 02 2006 - 08:05:53 CDT)
- TCL energy variables jbelof_at_mail.usf.edu (Sat Apr 01 2006 - 11:29:14 CST)
- dual core processors Leandro Martínez (Fri Mar 31 2006 - 11:04:01 CST)
- Molecular Volume Tamal Banerjee (Thu Mar 30 2006 - 22:22:26 CST)
- RE£º Re: how to plugin catDCD intoqVMD=20of=20windows=20version?= xiaojing gong (Wed Mar 29 2006 - 19:17:03 CST)
- bulk density in RDF.tcl ARTURAS ZIEMYS (Wed Mar 29 2006 - 10:28:44 CST)
- DCD file really corrupt? Lea Thøgersen (Wed Mar 29 2006 - 06:27:09 CST)
- how to plugin catDCD into VMD of windows version xiaojing gong (Wed Mar 29 2006 - 07:07:02 CST)
- Periodic cell has become too small Per Jr. Greisen (Wed Mar 29 2006 - 06:28:28 CST)
- Can I use namd for carbon nanotubes? Rob (Tue Mar 28 2006 - 22:16:44 CST)
- parameter files lily jin (Tue Mar 28 2006 - 14:13:39 CST)
- input file for PO3 lily jin (Tue Mar 28 2006 - 11:02:34 CST)
- Re£º Re: how to constrain a dihedralqangle=3F?= xiaojing gong (Tue Mar 28 2006 - 08:20:02 CST)
- Fwd: Re: vmd-l: Generating PSF for 1JNO.pdb chain A Lin (Mon Mar 27 2006 - 19:18:13 CST)
- force-field parameters for TOAC Gaurav Sharma (Mon Mar 27 2006 - 17:02:31 CST)
- no Na or CLA paramters in par_all22_prot.inp Shulin Zhuang (Mon Mar 27 2006 - 06:54:49 CST)
- psfgen operation for the C terminal of HSE Shulin Zhuang (Mon Mar 27 2006 - 01:46:57 CST)
- How to contract the PBC cell Tamal Banerjee (Mon Mar 27 2006 - 01:21:06 CST)
- about the MSE residue Shulin Zhuang (Sun Mar 26 2006 - 23:42:16 CST)
- MD problem bo baker (Sun Mar 26 2006 - 16:54:38 CST)
- Generating lipid bilayer model Gan, Yong (Sat Mar 25 2006 - 23:31:18 CST)
- MD Run frozen bo baker (Fri Mar 24 2006 - 15:42:47 CST)
- Tcl scripting within NAMD configuration file Chandra Ramananjara (Fri Mar 24 2006 - 09:26:18 CST)
- Simulation failed during the stage of heat Shulin Zhuang (Thu Mar 23 2006 - 23:58:15 CST)
- run frozen bo baker (Thu Mar 23 2006 - 20:08:58 CST)
- how to constrain a dihedral angle? xiaojing gong (Thu Mar 23 2006 - 18:55:34 CST)
- TCL scripting within NAMD Configuration File Chandra Ramananjara (Thu Mar 23 2006 - 09:12:56 CST)
- vmd-l: boubt about consistency of measures Sergio Anis (Thu Mar 23 2006 - 08:19:52 CST)
- force over selection Ioana Cozmuta (Wed Mar 22 2006 - 23:51:46 CST)
- Re: Gigabit ethernet switch for cluster Dow_Hurst (Wed Mar 22 2006 - 21:33:57 CST)
- SMD temperature scaling Christopher Calderon (Wed Mar 22 2006 - 17:09:44 CST)
- Use extendedSystem or cellBasisVector? Ching Wong (Wed Mar 22 2006 - 16:45:45 CST)
- energy calculation in VMD lily jin (Wed Mar 22 2006 - 16:41:45 CST)
- Can someone PLEASE explain the "firsttimestep" parameter ? Himanshu Khandelia (Wed Mar 22 2006 - 14:49:03 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? Sterling Paramore (Wed Mar 22 2006 - 15:40:02 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? Marcos Sotomayor (Wed Mar 22 2006 - 15:53:16 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? snoze pa (Wed Mar 22 2006 - 16:24:49 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? Himanshu Khandelia (Wed Mar 22 2006 - 16:45:17 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? surendra negi (Wed Mar 22 2006 - 18:19:39 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? Marcos Sotomayor (Wed Mar 22 2006 - 15:53:16 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? Brian Bennion (Wed Mar 22 2006 - 16:43:18 CST)
- Re: Can someone PLEASE explain the "firsttimestep" parameter ? Sterling Paramore (Wed Mar 22 2006 - 15:40:02 CST)
- using restart file or .coor/.vel file xiaojing gong (Wed Mar 22 2006 - 08:44:57 CST)
- Gigabit ethernet switch for cluster Cesar Luis Avila (Tue Mar 21 2006 - 14:43:45 CST)
- VMD Command Pijush Ghosh (Tue Mar 21 2006 - 00:00:42 CST)
- question about the parameter "exclude" xiaojing gong (Tue Mar 21 2006 - 07:20:31 CST)
- Re:Re:error caused by lipid membrane xiaojing gong (Mon Mar 20 2006 - 20:33:42 CST)
- error caused by atoms of lipid membrane xiaojing gong (Mon Mar 20 2006 - 06:27:07 CST)
- what does "patch" mean? xiaojing gong (Sun Mar 19 2006 - 20:04:25 CST)
- Re: error in membrane producing xiaojing gong (Sun Mar 19 2006 - 18:00:04 CST)
- the "firsttimestep" conundrum Himanshu Khandelia (Sun Mar 19 2006 - 15:20:47 CST)
- Building cluster Cesar Luis Avila (Sat Mar 18 2006 - 12:54:38 CST)
- error in membrane producing xiaojing gong (Fri Mar 17 2006 - 21:21:15 CST)
- error in membrane producing xiaojing gong (Fri Mar 17 2006 - 19:30:25 CST)
- Memory requirements for clusters Naresh (Fri Mar 17 2006 - 18:24:57 CST)
- problems with .conf script Pedro Borkowski (Fri Mar 17 2006 - 13:13:17 CST)
- Question about memory usage Joshua D. Moore (Fri Mar 17 2006 - 12:03:59 CST)
- timestep in namd snoze pa (Thu Mar 16 2006 - 12:34:10 CST)
- farnesyl&retinal Magda W (Thu Mar 16 2006 - 02:44:08 CST)
- Dihedral parameters for multiple minima Chang, Christopher (Wed Mar 15 2006 - 19:34:22 CST)
- compile error on amd64 in src/ComputeTclBC.C Sabuj Pattanayek (Wed Mar 15 2006 - 14:27:53 CST)
- difference in total energy values Osman Yogurtcu (Wed Mar 15 2006 - 13:59:44 CST)
- Equilibration with constant temperature and pressure santanu chatterjee (Tue Mar 14 2006 - 19:07:09 CST)
- command line arguments in NAMD ? Himanshu Khandelia (Tue Mar 14 2006 - 17:49:31 CST)
- MD in a loop with different names for dcd files Himanshu Khandelia (Tue Mar 14 2006 - 10:56:21 CST)
- during namd build / compile -ltcl8.4 linking error Sabuj Pattanayek (Mon Mar 13 2006 - 15:41:29 CST)
- Continue a run ? Georgios Papadopoulos (Mon Mar 13 2006 - 11:27:52 CST)
- possible error warning lily jin (Mon Mar 13 2006 - 12:48:58 CST)
- build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version Sabuj Pattanayek (Mon Mar 13 2006 - 12:31:56 CST)
- Re: build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version Sabuj Pattanayek (Mon Mar 13 2006 - 14:09:45 CST)
- Re: build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version Brian Bennion (Mon Mar 13 2006 - 14:18:15 CST)
- Re: build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version Gengbin Zheng (Tue Mar 14 2006 - 00:02:33 CST)
- Dumy atoms in FEP Raul Araya Secchi (Mon Mar 13 2006 - 09:13:22 CST)
- Question on simulation energy output Jason Lee (Sun Mar 12 2006 - 21:33:28 CST)
- area per lipid for a protein embedded membrane system M. Madhu (Fri Mar 10 2006 - 11:08:41 CST)
- FEP in vacuum Raul Araya Secchi (Fri Mar 10 2006 - 08:48:52 CST)
- RE: Aligning structures EPF \(Esben Peter Friis\) (Fri Mar 10 2006 - 01:34:40 CST)
- RE: is possible to remove the waterbox before running VMD Wolbach, Jeffrey P \(WOLBACH\) (Thu Mar 09 2006 - 13:45:20 CST)
- LES with PME and neutralizing charges curcio (Thu Mar 09 2006 - 11:48:41 CST)
- is possible to remove the waterbox before running VMD lily jin (Thu Mar 09 2006 - 10:34:02 CST)
- Re: is possible to remove the waterbox before running VMD Sterling Paramore (Thu Mar 09 2006 - 11:50:08 CST)
- Re: is possible to remove the waterbox before running VMD griadi_at_utalca.cl (Thu Mar 09 2006 - 12:56:38 CST)
- Re: vmd-l: is possible to remove the waterbox before running VMD John Stone (Thu Mar 09 2006 - 10:39:27 CST)
- Parameter resetting in NAMD Himanshu Khandelia (Thu Mar 09 2006 - 10:26:55 CST)
- a display problem lily jin (Thu Mar 09 2006 - 10:22:57 CST)
- volume exclusion Kyle Gustafson (Thu Mar 09 2006 - 09:51:30 CST)
- NAMD octahedron matteo filandri (Thu Mar 09 2006 - 07:57:54 CST)
- Pressure -ve Tamal Banerjee (Wed Mar 08 2006 - 08:49:57 CST)
- NAMD Linux LAM/MPI 7.1 execution error Christophe Combet [PBIL/IBCP/CNRS] (Tue Mar 07 2006 - 07:45:35 CST)
- RE: starting simulation in charmm, continuing in NAMD ? EPF \(Esben Peter Friis\) (Sun Mar 05 2006 - 14:35:18 CST)
- starting simulation in charmm, continuing in NAMD ? Himanshu Khandelia (Sun Mar 05 2006 - 11:23:15 CST)
- autocorrelation function ! Subhasish Chatterjee (Fri Mar 03 2006 - 20:17:56 CST)
- A question on simulation with NPT ensemble santanu chatterjee (Fri Mar 03 2006 - 13:18:34 CST)
- system rotates after equilibration Gordon Wells (Fri Mar 03 2006 - 03:21:30 CST)
- where to find the program DOWSER for setting water ? lily jin (Thu Mar 02 2006 - 15:33:03 CST)
- gradient for minimization Shirley Li (Thu Mar 02 2006 - 12:59:40 CST)
- Spherical harmonic restraint Morad Alawneh (Thu Mar 02 2006 - 11:39:48 CST)
- question about total charge change in FEP calculation jz7_at_duke.edu (Thu Mar 02 2006 - 10:01:23 CST)
- Re: question about total charge change in FEP calculation Chris Chipot (Sun Mar 05 2006 - 05:04:43 CST)
- Re: question about total charge change in FEP calculation jz7_at_duke.edu (Thu Jun 08 2006 - 10:16:23 CDT)
- please help-large energy change during FEP calculation jz7_at_duke.edu (Thu Jun 08 2006 - 12:13:31 CDT)
- Re: question about total charge change in FEP calculation Chris Chipot (Thu Jun 08 2006 - 14:47:27 CDT)
- Re: question about total charge change in FEP calculation jz7_at_duke.edu (Thu Jun 08 2006 - 15:28:21 CDT)
- Re: question about total charge change in FEP calculation Chris Chipot (Fri Jun 09 2006 - 02:05:46 CDT)
- Re: question about total charge change in FEP calculation Jerome Henin (Fri Jun 09 2006 - 10:20:01 CDT)
- unsubscribe Lin (Mon Jun 12 2006 - 09:45:23 CDT)
- Re: question about total charge change in FEP calculation jz7_at_duke.edu (Thu Jun 08 2006 - 10:16:23 CDT)
- Re: question about total charge change in FEP calculation Chris Chipot (Sun Mar 05 2006 - 05:04:43 CST)
- Re: question on membrane crushing Peter Freddolino (Thu Mar 02 2006 - 08:54:05 CST)
- Re: question on membrane crushing Marcos Sotomayor (Thu Mar 02 2006 - 08:32:34 CST)
- Re: question on membrane crushing Himanshu Khandelia (Thu Mar 02 2006 - 08:57:12 CST)
- Re: question on membrane crushing Arneh Babakhani (Fri Mar 03 2006 - 14:49:42 CST)
- Re: question on membrane crushing Arneh Babakhani (Mon Mar 13 2006 - 16:52:04 CST)
- question on membrane crushing Longzhu Shen (Thu Mar 02 2006 - 15:18:09 CST)
- radial distribution function Subhasish Chatterjee (Wed Mar 01 2006 - 16:01:44 CST)
- About Langevin Dynamics. Boyang Wang (Wed Mar 01 2006 - 12:18:30 CST)
- System after pressure change - confirmation needed ARTURAS ZIEMYS (Wed Mar 01 2006 - 09:30:20 CST)
- question about FEP calculation jz7_at_duke.edu (Wed Mar 01 2006 - 11:11:37 CST)
- namdstats gives nan's in tutorial output Jake Michaelson (Wed Mar 01 2006 - 10:40:48 CST)
- radial distribution function Leo.Ghemtio_at_sanofi-aventis.com (Wed Mar 01 2006 - 04:15:15 CST)
- (no subject) Michael Grabe (Tue Feb 28 2006 - 20:37:42 CST)
- NAMD2.6b1 on MAC cluster problems Michael Grabe (Tue Feb 28 2006 - 01:32:22 CST)
- NAMD2.6b1 on MACOSX Michael Grabe (Tue Feb 28 2006 - 12:04:12 CST)
- gradually pressure change (increase/decrease) ARTURAS ZIEMYS (Tue Feb 28 2006 - 11:44:08 CST)
- how gradually change (increase/decrease) pressure ? ARTURAS ZIEMYS (Mon Feb 27 2006 - 11:59:15 CST)
- Alchemical Free Energy Perturbation Jawahar Neelankatan (Sat Feb 25 2006 - 00:40:02 CST)
- radial distribution function Leo.Ghemtio_at_sanofi-aventis.com (Mon Feb 27 2006 - 08:23:42 CST)
- Re: question on pairinteraction Peter Freddolino (Sun Feb 26 2006 - 11:25:50 CST)
- question on pairinteraction Longzhu Shen (Sun Feb 26 2006 - 12:03:52 CST)
- Still problems with heating patrick wintrode (Sat Feb 25 2006 - 11:15:01 CST)
- tutorial address Georgios Papadopoulos (Sat Feb 25 2006 - 03:16:25 CST)
- Alchemical Free Energy Perturbation Jawahar Neelankatan (Sat Feb 25 2006 - 01:36:29 CST)
- About Langevin Damping Coefficient. Boyang Wang (Fri Feb 24 2006 - 17:57:24 CST)
- compile NAMD/CHARM on infiniband cluster Rene Salmon (Fri Feb 24 2006 - 16:20:16 CST)
- only minimization lily jin (Thu Feb 23 2006 - 18:11:22 CST)
- Unit of harmonic restraint force constant Leyla Celik (Fri Feb 24 2006 - 07:21:39 CST)
- Problem to run IMD simulation Laurent Leger (Fri Feb 24 2006 - 04:29:29 CST)
- namd and amber force field Fabien Cailliez (Thu Feb 23 2006 - 11:38:01 CST)
- (no subject) Michael Grabe (Wed Feb 22 2006 - 19:47:43 CST)
- waterbox snoze pa (Wed Feb 22 2006 - 10:57:12 CST)
- Electric Field jcm203_at_soton.ac.uk (Wed Feb 22 2006 - 10:17:39 CST)
- LES and minimalization Sławek Orłowski (Tue Feb 21 2006 - 02:42:06 CST)
- (no subject) Xiuping Tao (Thu Feb 16 2006 - 15:49:52 CST)
- NAMD not starting calculations... Jimmy Tang (Thu Feb 16 2006 - 08:00:34 CST)
- useGroupPressure snoze pa (Wed Feb 15 2006 - 15:48:55 CST)
- Re: question on mutate command in NAMD surendra negi (Wed Feb 15 2006 - 10:58:53 CST)
- question on mutate command in NAMD Longzhu Shen (Wed Feb 15 2006 - 16:49:19 CST)
- Problem heating the system patrick wintrode (Wed Feb 15 2006 - 08:37:16 CST)
- Re: HIS to HSD, HSE, and HSP John Eargle (Tue Feb 14 2006 - 17:05:33 CST)
- Pressure Driven flow of Water Wang, Boyang (Tue Feb 14 2006 - 15:14:02 CST)
- HIS to HSD, HSE, and HSP John Eargle (Tue Feb 14 2006 - 14:48:05 CST)
- charm++ over MPI Bogdan Costescu (Tue Feb 14 2006 - 11:07:19 CST)
- Free Cluster-Building Workshops - 16-17 Mar 2006, 20-21 Apr 2006 Tim Skirvin (Mon Feb 13 2006 - 14:41:24 CST)
- computer network snoze pa (Mon Feb 13 2006 - 11:26:51 CST)
- how to make dual-hybrid topology? Indrajaya (Mon Feb 13 2006 - 06:47:21 CST)
- Problem with VMD 'animate' command Chandra Ramananjara (Sun Feb 12 2006 - 10:12:36 CST)
- Rattle Error During Equilibration of Lipid Bilayer Membrane Arneh Babakhani (Fri Feb 10 2006 - 22:32:51 CST)
- Re: Rattle Error During Equilibration of Lipid Bilayer Membrane Morad Alawneh (Sat Feb 11 2006 - 09:49:07 CST)
- Re: Rattle Error During Equilibration of Lipid Bilayer Membrane Arneh Babakhani (Wed Feb 22 2006 - 14:09:23 CST)
- Jump in Electrostatic Energy between two values M. Madhu (Fri Feb 10 2006 - 14:33:17 CST)
- extra lines in PSF !!! Georgios Papadopoulos (Fri Feb 10 2006 - 11:47:10 CST)
- Fwd: Water Box size snoze pa (Fri Feb 10 2006 - 10:58:27 CST)
- Re: Fwd: Water Box size Marc Q. Ma (Fri Feb 10 2006 - 12:40:50 CST)
- Re: Fwd: Water Box size Philip Blood (Fri Feb 10 2006 - 13:37:54 CST)
- Re: Fwd: Water Box size snoze pa (Fri Feb 10 2006 - 13:49:07 CST)
- Fwd: Fwd: Water Box size snoze pa (Wed Feb 15 2006 - 11:29:19 CST)
- Re: Fwd: Water Box size snoze pa (Wed Feb 15 2006 - 11:58:33 CST)
- Re: Fwd: Water Box size L. Michel Espinoza-Fonseca (Wed Feb 15 2006 - 12:23:26 CST)
- Re: Fwd: Water Box size L. Michel Espinoza-Fonseca (Wed Feb 15 2006 - 12:00:51 CST)
- Re: Fwd: Water Box size snoze pa (Fri Feb 10 2006 - 13:49:07 CST)
- pairInteractionSelf Yu Wang (Fri Feb 10 2006 - 03:19:34 CST)
- Buffering problems while attempting to read log file Zach Hensel (Fri Feb 10 2006 - 11:08:29 CST)
- I want to know how to make pdb file with 2d structrure file. Taeho Kim (Fri Feb 10 2006 - 02:14:31 CST)
- Re: unusual, periodic crash in Linux FC3/GM/MPI/CHARM/NAMD Dan Strahs (Thu Feb 09 2006 - 18:41:29 CST)
- unusual, periodic crash in Linux FC3/GM/MPI/CHARM/NAMD Dan Strahs (Thu Feb 09 2006 - 17:01:30 CST)
- RE: [Fwd: SMD of titin domain] Mu Gao (Wed Feb 08 2006 - 19:23:29 CST)
- Modeling HCN. Boyang Wang (Wed Feb 08 2006 - 18:47:14 CST)
- How to model HCN gas molecule by NAMD? Boyang Wang (Wed Feb 08 2006 - 18:44:42 CST)
- Amber Parameter in NAMD snoze pa (Wed Feb 08 2006 - 18:42:00 CST)
- [Fwd: increasing RMSD after 2 ns minimization-equilibration] dora guzman (Wed Feb 08 2006 - 17:05:51 CST)
- [Fwd: SMD of titin domain] dora guzman (Wed Feb 08 2006 - 17:05:34 CST)
- Topology file for Building Gramicidin A (tutorial) M. Madhu (Tue Feb 07 2006 - 11:37:13 CST)
- Socket closed before recv. Leandro Martínez (Tue Feb 07 2006 - 05:18:05 CST)
- question on membrane simulation Longzhu Shen (Tue Feb 07 2006 - 11:03:43 CST)
- Question on the bond energy of NAMD tutorial Jason Lee (Mon Feb 06 2006 - 15:51:22 CST)
- Problem with center of mass movement in simulation rwiese_at_unr.edu (Mon Feb 06 2006 - 12:01:21 CST)
- patch in psfgen... Navratna Vajpai (Mon Feb 06 2006 - 11:37:14 CST)
- DNA protonation mustapha.hamdi_at_ensi-bourges.fr (Mon Feb 06 2006 - 05:04:53 CST)
- About "mutate" command in psfgen package. Boyang Wang (Thu Feb 02 2006 - 17:24:42 CST)
- dublicated residue numbers in PDB/PSF ARTURAS ZIEMYS (Wed Feb 01 2006 - 09:14:53 CST)
- Tools to "open" domains ARTURAS ZIEMYS (Tue Jan 31 2006 - 10:12:03 CST)
- How to get different kinds of harmonic constraints in one script? Morad Alawneh (Tue Jan 31 2006 - 09:48:21 CST)
- Can any one help me with this parallel issue Morad Alawneh (Sun Jan 29 2006 - 18:17:06 CST)
- NAMD hangs in parallel on OSX Michael Grabe (Fri Jan 27 2006 - 12:37:38 CST)
- NAMD with Myrinet MX on MacOS X Goran Krilov (Fri Jan 27 2006 - 11:35:54 CST)
- Trying to profile namd to look for memory leaks Scott Atchley (Fri Jan 27 2006 - 10:33:04 CST)
- IMD-host name-port number-connection problem. rakesh... (Thu Jan 26 2006 - 15:54:43 CST)
- Berendsen pressure control problem Jason Lee (Thu Jan 26 2006 - 14:15:29 CST)
- NBFix not working with charmm par file Giovanni Bellesia (Wed Jan 25 2006 - 17:36:03 CST)
- dihedrals multiplicity in xplor psf file Giovanni Bellesia (Wed Jan 25 2006 - 15:12:16 CST)
- hybrid qm/mm Jake Michaelson (Wed Jan 25 2006 - 15:14:47 CST)
- namd2.6b1 has bad scaling Morad Alawneh (Wed Jan 25 2006 - 11:17:53 CST)
- How to create psf for carbohydrate jas theway (Mon Jan 23 2006 - 19:02:13 CST)
- NAMD at NCSA snoze pa (Tue Jan 24 2006 - 11:09:31 CST)
- Problem with biotin autopsf Lin (Tue Jan 24 2006 - 08:14:15 CST)
- question on 1-4scaling factor Hyonseok Hwang (Sun Jan 22 2006 - 22:58:24 CST)
- margin error message surendra negi (Sat Jan 21 2006 - 12:23:01 CST)
- Saving coordinates of each frame into one separate .pdb file from a 100-frame .dcd file. Boyang Wang (Fri Jan 20 2006 - 10:44:36 CST)
- question on the format of adding Lennard-Jones parameters Hyonseok Hwang (Thu Jan 19 2006 - 19:06:54 CST)
- Problem with NAMD and constraint failures rwiese_at_unr.edu (Thu Jan 19 2006 - 18:27:11 CST)
- NAMD memory problems on ASC's SGI Altix machine Sterling Paramore (Thu Jan 19 2006 - 10:46:33 CST)
- peptides confined in a water sphere Giovanni Bellesia (Thu Jan 19 2006 - 09:37:01 CST)
- Configurational temperature - coordinates Alexe Bojovschi (Wed Jan 18 2006 - 21:11:32 CST)
- wrong simulation times or misleading time counting? Carlos Simoes (Wed Jan 18 2006 - 17:48:59 CST)
- atom restraints jsachs_at_mail.csb.yale.edu (Wed Jan 18 2006 - 15:02:26 CST)
- MMTools/PCA Richard Wood (Wed Jan 18 2006 - 12:13:00 CST)
- question on membrane protein simulation Longzhu Shen (Wed Jan 18 2006 - 04:56:44 CST)
- PSF file Jindal Shah (Tue Jan 17 2006 - 13:21:49 CST)
- how to install rmsdtt in Windows... seonah kim (Tue Jan 17 2006 - 09:52:00 CST)
- Compiled NAMD on SGI Altix Sterling Paramore (Mon Jan 16 2006 - 18:51:18 CST)
- Multi Harmonic constrains Morad Alawneh (Mon Jan 16 2006 - 11:01:00 CST)
- which force field to choose Wei Zhuang (Sat Jan 14 2006 - 14:02:25 CST)
- help-minimization and equilibration of Ubiquitin in a water box Zhi Qi (Thu Jan 12 2006 - 18:38:00 CST)
- NAMD fails on Altix Margaret Kahn (Wed Jan 11 2006 - 19:50:44 CST)
- help-minimization and equilibration of Ubiquitin in a water box Zhi Qi (Wed Jan 11 2006 - 14:13:45 CST)
- variable cellOrigin Hugo Azurmendi (Wed Jan 11 2006 - 15:49:30 CST)
- generation of non-standart charmm topology ziemys_at_ecr6.ohio-state.edu (Wed Jan 11 2006 - 12:08:12 CST)
- simulation and equilibration bo baker (Tue Jan 10 2006 - 16:00:19 CST)
- Re: reading a binary restart file Leandro Martínez (Tue Jan 10 2006 - 16:10:31 CST)
- velocity error, still bo baker (Tue Jan 10 2006 - 15:20:58 CST)
- reading a binary restart file Leandro Martínez (Tue Jan 10 2006 - 13:09:18 CST)
- Re: updating TCL version for NAMD? Dan Strahs (Mon Jan 09 2006 - 11:18:16 CST)
- About "get z" command in MD script language. Boyang Wang (Sat Jan 07 2006 - 20:57:08 CST)
- Re: Turning off forces in VMD Richard Wood (Sun Jan 08 2006 - 17:03:28 CST)
- Re: Simulation in vaccum bo baker (Fri Jan 06 2006 - 22:12:40 CST)
- Simulation in vaccum bo baker (Fri Jan 06 2006 - 19:17:03 CST)
- updating TCL version for NAMD? Dan Strahs (Fri Jan 06 2006 - 17:42:35 CST)
- same random numbers?? Shahid Qamar (Fri Jan 06 2006 - 15:49:01 CST)
- problems reading large dcd file Jorge Pikunic (Fri Jan 06 2006 - 10:45:54 CST)
- AutoIMD Richard Wood (Fri Jan 06 2006 - 12:36:03 CST)
- Re: problems reading large dcd file Joshua D. Moore (Fri Jan 06 2006 - 23:22:43 CST)
- RE: problems reading large dcd file Jorge Pikunic (Tue Jan 10 2006 - 10:20:35 CST)
- RE: problems reading large dcd file Michel Espinoza-Fonseca (Tue Jan 10 2006 - 10:59:14 CST)
- RE: problems reading large dcd file Joshua D. Moore (Tue Jan 10 2006 - 19:35:55 CST)
- RE: problems reading large dcd file Jorge Pikunic (Wed Jan 11 2006 - 09:06:59 CST)
- RE: problems reading large dcd file Joshua D. Moore (Fri Jan 13 2006 - 21:32:42 CST)
- 64 bit NAMD on AIX and CatDCD Joshua D. Moore (Sat Jan 21 2006 - 13:22:11 CST)
- Re: vmd-l: 64 bit NAMD on AIX and CatDCD John Stone (Mon Jan 23 2006 - 13:21:14 CST)
- RE: problems reading large dcd file Jorge Pikunic (Tue Jan 10 2006 - 10:20:35 CST)
- Re: problems reading large dcd file Alessandro Pedretti (Sat Jan 07 2006 - 04:14:55 CST)
- What's the highest temperature I can go? Dong Luo (Thu Jan 05 2006 - 13:11:19 CST)
- Atom distance & ptraj bo baker (Thu Jan 05 2006 - 11:47:46 CST)
- PSFGEN for protein containing GTP Shirley Li (Wed Jan 04 2006 - 21:55:13 CST)
- psfgen problem Morad Alawneh (Wed Jan 04 2006 - 17:34:46 CST)
- atom distances bo baker (Wed Jan 04 2006 - 14:17:29 CST)
- velocity error bo baker (Wed Jan 04 2006 - 13:12:45 CST)
- CMAP problem Morad Alawneh (Tue Jan 03 2006 - 13:45:41 CST)
- Energy Plugin bo baker (Mon Jan 02 2006 - 18:54:12 CST)
- FEP setup Richard Wood (Tue Dec 27 2005 - 11:43:53 CST)
- About the Source code. Boyang Wang (Mon Dec 26 2005 - 21:40:56 CST)
- How does NAMD calculate Electrostatic potential energy (no periodic boundary condition)? Boyang Wang (Mon Dec 26 2005 - 17:46:55 CST)
- NAMD Energy Plugin bo baker (Tue Dec 27 2005 - 18:15:40 CST)
- Re: vmd-l: convert DCD files to CRD format Angel Gonzalez Wong (Mon Dec 26 2005 - 09:19:53 CST)
- Can extending MIN solve the problem of "Constraint failure in RATTLE algorithm" Shirley Li (Sat Dec 24 2005 - 12:58:55 CST)
- Dose restart frequently affect the results? liu xin (Fri Dec 23 2005 - 21:33:40 CST)
- FATAL ERROR: unknown floating-point error, errno = 4 Manori Indira Jayasinghe (Thu Dec 22 2005 - 23:16:41 CST)
- Re: FATAL ERROR: unknown floating-point error, errno = 4 Chris Chipot (Fri Dec 23 2005 - 01:22:32 CST)
- UNABLE TO OPEN .psf FILE Joshua D. Moore (Fri Dec 23 2005 - 02:53:00 CST)
- preparing a dimeric protein for NAMD Irene Newhouse (Thu Dec 22 2005 - 21:28:21 CST)
- Question about Generating DCD files with only specified atoms Joshua D. Moore (Thu Dec 22 2005 - 18:06:09 CST)
- The HT-HT-OT angle parameter for TIP3? Shirley Li (Thu Dec 22 2005 - 14:57:19 CST)
- Locally Enhanced Sampling milton sonoda (Wed Dec 21 2005 - 17:34:23 CST)
- Kinetic Energy difference using restart binaries Mikolai Fajer (Wed Dec 21 2005 - 12:54:13 CST)
- FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7 Shirley Li (Wed Dec 21 2005 - 14:56:36 CST)
- Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7 Joshua D. Moore (Wed Dec 21 2005 - 16:57:37 CST)
- The angle parameters for CN7 are missing in NAMD? Shirley Li (Wed Dec 21 2005 - 18:02:07 CST)
- UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Shirley Li (Thu Dec 22 2005 - 13:16:00 CST)
- Re: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Peter Freddolino (Thu Dec 22 2005 - 14:35:37 CST)
- Re: ANGLE PARAMETERS (It works now) Shirley Li (Thu Dec 22 2005 - 16:54:06 CST)
- Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7 Joshua D. Moore (Wed Dec 21 2005 - 16:57:37 CST)
- FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7 Shirley Li (Wed Dec 21 2005 - 14:56:36 CST)
- PSF file format Jindal Shah (Tue Dec 20 2005 - 15:55:23 CST)
- define abf1 and abf2 for CM of water and CM of molecule Manori Indira Jayasinghe (Mon Dec 19 2005 - 22:53:42 CST)
- flipDCD and Unit Cell information? Joshua D. Moore (Mon Dec 19 2005 - 17:54:06 CST)
- checking for correct construction of dihedrals, etc. Ralph Jimenez (Mon Dec 19 2005 - 16:51:52 CST)
- RE: charmm27 fatal error Michel Espinoza-Fonseca (Mon Dec 19 2005 - 15:30:41 CST)
- charmm27 fatal error Arturas Ziemys (Mon Dec 19 2005 - 14:06:00 CST)
- NAMD/CHARM source installation option Jyh-Shyong Ho (Sat Dec 17 2005 - 23:36:55 CST)
- extra points in NAMD Mgr. Lubos Vrbka (Sat Dec 17 2005 - 06:51:46 CST)
- Some warnings from log file after minimization Grace Shen (Fri Dec 16 2005 - 13:05:53 CST)
- pause simulation Leandro Martínez (Fri Dec 16 2005 - 12:53:23 CST)
- Some problem on compiling NAMD ËïÍ¥¹ã (Thu Dec 15 2005 - 21:24:18 CST)
- Atom Positions during simulation Francisco Castro (Wed Dec 14 2005 - 16:27:12 CST)
- return molecule to its principal axes mpavlova_at_purdue.edu (Wed Dec 14 2005 - 13:54:32 CST)
- Counterions: how to decide how many to put it? Ching Wong (Tue Dec 13 2005 - 17:44:33 CST)
- RE: NAMD on Win64 Michel Espinoza-Fonseca (Mon Dec 12 2005 - 10:53:19 CST)
- NAMD on Win64 Lea Thøgersen (Mon Dec 12 2005 - 10:26:11 CST)
- center of mass motion: problems Vani Krishna (Thu Dec 08 2005 - 16:27:06 CST)
- Reading from DCD file and running MD Shahid Qamar (Wed Dec 07 2005 - 14:35:05 CST)
- Packaging 100 cations and anions in a box ir7_at_njit.edu (Tue Dec 06 2005 - 22:47:56 CST)
- Atoms moving too fast Eric Perim (Tue Dec 06 2005 - 13:05:10 CST)
- successive minimization with different sets of fixed atoms JIMENEZ Ralph (Tue Dec 06 2005 - 11:14:25 CST)
- A question regarding generate pdb and psf file Grace Shen (Tue Dec 06 2005 - 11:06:27 CST)
- Chamrun/NAMD processes and PBS cluster Nicolas Sapay (Mon Dec 05 2005 - 07:55:15 CST)
- how is NAMD output written in parallel mode? Ravinder Abrol (Mon Dec 05 2005 - 02:09:38 CST)
- Adding amino acids to an existing pdb structure LEWYN LI (Sun Dec 04 2005 - 21:30:49 CST)
- restart problem liu xin (Fri Dec 02 2005 - 00:01:26 CST)
- Problems opening the Extended Trajectory File Eric Perim (Thu Dec 01 2005 - 13:36:36 CST)
- Warning in namd output file Uma Mahankali (Wed Nov 30 2005 - 18:27:48 CST)
- merge trajectory from NAMD michael jerry (Wed Nov 30 2005 - 16:19:57 CST)
- problem with the NAMD CPU time consumption on a batch queueing system Nicolas Sapay (Mon Nov 28 2005 - 11:46:08 CST)
- Water Box Shrinks Ching Wong (Fri Nov 25 2005 - 19:10:46 CST)
- Update on Implicit Solvent Models in NAMD? Joshua D. Moore (Fri Nov 25 2005 - 14:01:31 CST)
- Interaction between metal and metal-water. Taeho Kim (Fri Nov 25 2005 - 10:39:22 CST)
- CHARMM compatible Methotrexate params Aaron Oakley (Thu Nov 24 2005 - 22:17:18 CST)
- RE: Na ions got into the catalytic site during Production Run Michel Espinoza-Fonseca (Mon Nov 21 2005 - 10:16:38 CST)
- Namd2.6b1 FATAL ERROR: Memory allocation failed on AIX53 IBM-SP4 Sascha Tayefeh (Mon Nov 21 2005 - 02:56:34 CST)
- Na ions got into the catalytic site during Production Run Ching Wong (Sun Nov 20 2005 - 17:34:01 CST)
- temperature "coupling coefficient" in NAMD curcio (Fri Nov 18 2005 - 11:09:13 CST)
- Replica-Exchange MD Marc Baaden (Fri Nov 18 2005 - 03:18:19 CST)
- The psf format conversion Grace Shen (Wed Nov 16 2005 - 16:54:42 CST)
- freeEnergy of conformational change of a test molecule Uma Mahankali (Wed Nov 16 2005 - 13:33:18 CST)
- NAMD on Intel XEON EM64T Sterling Paramore (Mon Nov 14 2005 - 16:55:50 CST)
- munch: The input file main.o is not valid in the current object mode Raj NK (Mon Nov 14 2005 - 16:14:36 CST)
- parameter and topology for 4-MI arijit_r_at_chem.iitkgp.ernet.in (Mon Nov 14 2005 - 00:19:27 CST)
- Problem with NAMD on Opteron cluster tepper_at_amolf.nl (Fri Nov 11 2005 - 10:36:39 CST)
- Errors: Periodic cell became too small for original patch grid & Setting parameter binaryoutput from script failed! Nitin Bhardwaj (Sun Nov 13 2005 - 12:26:35 CST)
- Problem with NAMD on Opteron cluster Harald Tepper (Sat Nov 12 2005 - 05:29:33 CST)
- ABF for conformational analysis Uma Mahankali (Fri Nov 11 2005 - 16:54:11 CST)
- FEP.... Raul Araya Secchi (Fri Nov 11 2005 - 09:39:41 CST)
- Pair Interaction options Uma Mahankali (Thu Nov 10 2005 - 10:20:24 CST)
- Energy for part of system Ralph Jimenez (Wed Nov 09 2005 - 16:55:14 CST)
- Different solvents Gaurav Sharma (Tue Nov 08 2005 - 13:09:27 CST)
- General question about NAMD michael jerry (Tue Nov 08 2005 - 10:52:04 CST)
- Problem with compiling NAMD on Suse 9.3 fu guoxing (Tue Nov 08 2005 - 06:23:10 CST)
- PMF calculation using fixed restraints Vani Krishna (Sun Nov 06 2005 - 12:26:22 CST)
- NAMD 2.6 in IBM SP Xinghua Shi (Sat Nov 05 2005 - 09:41:35 CST)
- NAMD 2.6 in IBM SP Xinghua Shi (Sat Nov 05 2005 - 09:12:12 CST)
- restart a simulation Shirley Li (Fri Nov 04 2005 - 16:15:35 CST)
- A question on minimization santanu chatterjee (Fri Nov 04 2005 - 15:44:32 CST)
- The vector direction in SMD Grace Shen (Fri Nov 04 2005 - 15:01:51 CST)
- Size of water box santanu chatterjee (Fri Nov 04 2005 - 13:06:07 CST)
- RE: namd: advice Grace Shen (Fri Nov 04 2005 - 09:20:13 CST)
- namd: advice Sergio Anis (Fri Nov 04 2005 - 07:56:34 CST)
- questions about applying patches Ralph Jimenez (Thu Nov 03 2005 - 14:23:27 CST)
- RE: more Heme troubles Ralph Jimenez (Thu Nov 03 2005 - 13:19:54 CST)
- Increasing temp during MD Grace Shen (Thu Nov 03 2005 - 12:11:27 CST)
- How to atomselect several residues Grace Shen (Wed Nov 02 2005 - 17:28:50 CST)
- ERROR: Constraint failure in RATTLE algorithm for atom 598! Raul Araya Secchi (Wed Nov 02 2005 - 08:17:29 CST)
- How to patch segments of aminoacids Alexe Bojovschi (Wed Nov 02 2005 - 03:09:08 CST)
- IC Removal and Problem Nara Dashdorj (Tue Nov 01 2005 - 22:31:53 CST)
- POPC or POPE? Charles Danko (Tue Nov 01 2005 - 22:20:04 CST)
- ABF.TCl file ??? Shahid Qamar (Tue Nov 01 2005 - 13:56:25 CST)
- CA CL CA angle? Richard Wood (Tue Nov 01 2005 - 11:11:44 CST)
- RE: About ADP Michel Espinoza-Fonseca (Tue Nov 01 2005 - 10:16:43 CST)
- About ADP Grace Shen (Tue Nov 01 2005 - 09:48:43 CST)
- Replica-Exchange MD Mark Abraham (Mon Oct 31 2005 - 22:57:17 CST)
- Question regarding SMD Grace Shen (Mon Oct 31 2005 - 15:11:01 CST)
- beta-peptides ... Nicholas M Glykos (Mon Oct 31 2005 - 06:34:20 CST)
- How can I increase the computing rate on the computer cluster xiaojing gong (Sun Oct 30 2005 - 05:44:24 CST)
- Fwd: All or Nothing at All?? griadi_at_utalca.cl (Sat Oct 29 2005 - 14:02:12 CDT)
- All or Nothing at All?? Angelo R. Rossi (Sat Oct 29 2005 - 11:41:32 CDT)
- questions about running namd on NCSA cluster tungsten Wei Zhuang (Fri Oct 28 2005 - 17:09:22 CDT)
- About RMSD calculation. Boyang Wang (Fri Oct 28 2005 - 10:49:14 CDT)
- Myrinet NAMD Wei Zhuang (Fri Oct 28 2005 - 14:01:21 CDT)
- new problem Richard Wood (Thu Oct 27 2005 - 21:52:17 CDT)
- (no subject) Michael Grabe (Thu Oct 27 2005 - 22:39:35 CDT)
- urestraint doesn't work Wei Zhuang (Thu Oct 27 2005 - 16:56:55 CDT)
- RE: How to append charmm stream file Michel Espinoza-Fonseca (Wed Oct 26 2005 - 12:36:01 CDT)
- How to append charmm stream file Grace Shen (Wed Oct 26 2005 - 12:01:23 CDT)
- Only part of the protein is moving in MD simulation Uma Mahankali (Wed Oct 26 2005 - 10:12:13 CDT)
- RE: trying to generate a peptide Michel Espinoza-Fonseca (Wed Oct 26 2005 - 03:35:23 CDT)
- fixed atoms Gan, Yong \(UMC-Student\) (Tue Oct 25 2005 - 23:18:59 CDT)
- trying to generate a peptide Richard Wood (Tue Oct 25 2005 - 20:07:01 CDT)
- Can I miminimize some atoms in system Shahid Qamar (Tue Oct 25 2005 - 16:40:06 CDT)
- saving coordinates as a PDB file after minimization in NAMD Richard Wood (Tue Oct 25 2005 - 13:12:02 CDT)
- Re: saving coordinates as a PDB file after minimization in NAMD Richard Law (Tue Oct 25 2005 - 15:44:17 CDT)
- Box size Gan, Yong \(UMC-Student\) (Tue Oct 25 2005 - 11:50:06 CDT)
- Assign the ligand force field parameters Grace Shen (Mon Oct 24 2005 - 16:32:13 CDT)
- Water Sphere Raul Araya Secchi (Mon Oct 24 2005 - 15:21:27 CDT)
- Serious Steric Atom Clashes Nara Dashdorj (Sun Oct 23 2005 - 13:45:43 CDT)
- scaling issue Robert Bjornson (Fri Oct 21 2005 - 15:56:13 CDT)
- Question about load balancing Robert Bjornson (Fri Oct 21 2005 - 15:44:46 CDT)
- (no subject) Shahid Qamar (Fri Oct 21 2005 - 11:20:08 CDT)
- Can NAMD control pressure gradually increase? weikai (Fri Oct 21 2005 - 02:30:41 CDT)
- Gromacs parameters in NAMD Kasson (Thu Oct 20 2005 - 13:21:06 CDT)
- (no subject) Michael Grabe (Wed Oct 19 2005 - 19:09:19 CDT)
- SGE (Grid Engine) on Rocks Cluster Mauricio Carrillo Tripp (Wed Oct 19 2005 - 17:27:57 CDT)
- (no subject) Michael Grabe (Wed Oct 19 2005 - 14:53:14 CDT)
- How to run namd on NCSA Tungsten snoze pa (Wed Oct 19 2005 - 14:38:58 CDT)
- Warning: add bond failed in patch of ACE Per Jr. Greisen (Wed Oct 19 2005 - 14:14:24 CDT)
- NAMD on myrinet Hyonseok Hwang (Tue Oct 18 2005 - 16:12:36 CDT)
- Compilation of NAMD on 64-bit NUMA with icc ashwin joshi (Tue Oct 18 2005 - 02:46:18 CDT)
- A question on psfgen santanu chatterjee (Tue Oct 18 2005 - 01:55:39 CDT)
- running NAMD on tungsten Wei Zhuang (Tue Oct 18 2005 - 01:59:57 CDT)
- PSF file ATP Per Jr. Greisen (Sat Oct 15 2005 - 15:01:36 CDT)
- How to have neutral terminal ends eladp_at_hplus.tau.ac.il (Sat Oct 15 2005 - 04:15:01 CDT)
- PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP Troy Wymore (Fri Oct 14 2005 - 13:18:27 CDT)
- ATP PDB file Per Jr. Greisen (Fri Oct 14 2005 - 07:25:40 CDT)
- ATP nucleotides using NAMD greisen_at_binf.ku.dk (Fri Oct 14 2005 - 04:56:45 CDT)
- CMAP in VMD error greisen_at_binf.ku.dk (Thu Oct 13 2005 - 15:58:33 CDT)
- Metal Ion and Protein binding Gaurav Sharma (Thu Oct 13 2005 - 12:23:23 CDT)
- NAMD distribute Dan Strahs (Wed Oct 12 2005 - 20:28:49 CDT)
- Question about cutoff distance Leonardo Sepulveda Durán (Tue Oct 11 2005 - 17:06:10 CDT)
- make namd2 problem prodakt_at_o2.pl (Wed Oct 12 2005 - 06:21:53 CDT)
- NAMD restarts binary files snoze pa (Wed Oct 12 2005 - 10:21:46 CDT)
- gcc4 Gianluca Interlandi (Tue Oct 11 2005 - 16:34:32 CDT)
- running NAMD2 in parallel Gan, Yong \(UMC-Student\) (Tue Oct 11 2005 - 10:42:42 CDT)
- RE: running NAMD2 in parallel Gan, Yong \(UMC-Student\) (Mon Oct 10 2005 - 22:34:32 CDT)
- running NAMD2 in parallel Gan, Yong \(UMC-Student\) (Mon Oct 10 2005 - 21:23:46 CDT)
- problem with PSFGEN Shirley Li (Mon Oct 10 2005 - 18:15:58 CDT)
- namdplot: command not found bo baker (Mon Oct 10 2005 - 17:36:32 CDT)
- Re: namdplot: command not found Pawel Weronski (Tue Oct 11 2005 - 08:22:18 CDT)
- Re: namdplot: command not found Robert Brunner (Tue Oct 11 2005 - 10:32:00 CDT)
- Re: namdplot: command not found bo baker (Tue Oct 11 2005 - 18:56:10 CDT)
- Re: namdplot: command not found bo baker (Wed Oct 12 2005 - 15:27:23 CDT)
- Re: namdplot: command not found bo baker (Thu Oct 13 2005 - 14:26:47 CDT)
- Re: namdplot: command not found Sterling Paramore (Thu Oct 13 2005 - 14:59:36 CDT)
- Re: namdplot: command not found Robert Brunner (Thu Oct 13 2005 - 15:11:37 CDT)
- Re: namdplot: command not found bo baker (Fri Oct 14 2005 - 14:04:53 CDT)
- Re: namdplot: command not found Brian Bennion (Fri Oct 14 2005 - 14:44:14 CDT)
- Re: namdplot: command not found Brian Bennion (Thu Oct 13 2005 - 16:09:03 CDT)
- Re: namdplot: command not found bo baker (Mon Oct 17 2005 - 19:50:01 CDT)
- Re: namdplot: command not found Pawel Weronski (Tue Oct 11 2005 - 08:22:18 CDT)
- fix backbone atom bo baker (Sun Oct 09 2005 - 01:52:35 CDT)
- developing parameters for charmm snoze pa (Sat Oct 08 2005 - 19:40:54 CDT)
- reconstruct PMF akash.khandelwal_at_ndsu.edu (Sat Oct 08 2005 - 15:54:26 CDT)
- Recalculating energies from DCD file Chang, Christopher (Fri Oct 07 2005 - 18:05:37 CDT)
- Running NAMD 2.6b1 on Linux Networks Gan, Yong \(UMC-Student\) (Fri Oct 07 2005 - 16:44:53 CDT)
- NAMD 2.6b1 error writing DCD file on Cray XT3 Philip Blood (Fri Oct 07 2005 - 13:24:47 CDT)
- topology and parameter for acetylcholine Michel Espinoza-Fonseca (Fri Oct 07 2005 - 06:28:38 CDT)
- Penetration of water bo baker (Fri Oct 07 2005 - 00:20:46 CDT)
- About the potential of NAMD yangbing00_at_mails.tsinghua.edu.cn (Thu Oct 06 2005 - 22:53:46 CDT)
- About the potantial of IONS yangbing00_at_mails.tsinghua.edu.cn (Thu Oct 06 2005 - 22:16:17 CDT)
- command to run MPI and ABF Shahid Qamar (Thu Oct 06 2005 - 18:10:39 CDT)
- more heme troubles JIMENEZ Ralph (Thu Oct 06 2005 - 16:14:45 CDT)
- autoionize and psfgen, which one first? Shirley Li (Thu Oct 06 2005 - 16:01:42 CDT)
- VMD scripting Shirley Li (Thu Oct 06 2005 - 14:33:21 CDT)
- rigid bonds for other atoms Kyle Gustafson (Thu Oct 06 2005 - 13:40:23 CDT)
- namd 2.6b1 Gan, Yong \(UMC-Student\) (Wed Oct 05 2005 - 20:50:57 CDT)
- Does NAMD calculate the potential energy of FIXED ATOMS? Boyang Wang (Wed Oct 05 2005 - 12:14:36 CDT)
- difficulties using SMD on atoms in large systems Philip Blood (Tue Oct 04 2005 - 12:42:01 CDT)
- help generating psf files Richard Wood (Tue Oct 04 2005 - 11:37:08 CDT)
- Re: help generating psf files Peter Freddolino (Wed Oct 05 2005 - 22:09:07 CDT)
- Re: help generating psf files Anna Modzelewska (Thu Oct 06 2005 - 02:37:14 CDT)
- 1-4 interactions scaling Mauricio Carrillo Tripp (Mon Oct 03 2005 - 14:30:00 CDT)
- About calculating RMSD with rmsd.tcl Boyang Wang (Fri Sep 30 2005 - 19:55:26 CDT)
- Re water box and system charge Boyang Wang (Fri Sep 30 2005 - 19:47:16 CDT)
- namd cluster run, connection refused snoze pa (Thu Sep 29 2005 - 20:06:57 CDT)
- ensemble Wei Chen (Wed Oct 05 2005 - 16:34:12 CDT)
- psfgen trouble with heme JIMENEZ Ralph (Wed Oct 05 2005 - 14:54:26 CDT)
- Question about cutoff distance Leonardo Sepulveda Durán (Wed Oct 05 2005 - 12:56:24 CDT)
- ABF Simulation Lionel Perrin (Wed Oct 05 2005 - 06:41:44 CDT)
- Re: ABF Simulation Chris Chipot (Wed Oct 05 2005 - 07:58:57 CDT)
- Re: ABF Simulation Lionel Perrin (Thu Oct 06 2005 - 09:13:45 CDT)
- Re: ABF Simulation Jérôme Hénin (Wed Oct 19 2005 - 04:11:17 CDT)
- Re: ABF Simulation Lionel Perrin (Fri Oct 21 2005 - 04:03:02 CDT)
- Re: ABF Simulation Lionel Perrin (Wed Oct 26 2005 - 10:52:53 CDT)
- Re: ABF Simulation Jérôme Hénin (Fri Oct 28 2005 - 04:05:52 CDT)
- Re: ABF Simulation Lionel Perrin (Wed Nov 02 2005 - 08:28:25 CST)
- Re: ABF Simulation Tyler Luchko (Mon Jun 26 2006 - 19:45:02 CDT)
- Re: ABF Simulation Giovanni Bellesia (Mon Jun 26 2006 - 21:29:24 CDT)
- Re: ABF Simulation Tyler Luchko (Thu Jun 29 2006 - 00:11:42 CDT)
- Re: ABF Simulation Lionel Perrin (Tue Jun 27 2006 - 03:47:16 CDT)
- Re: ABF Simulation Lionel Perrin (Thu Oct 06 2005 - 09:13:45 CDT)
- Re: ABF Simulation Jérôme Hénin (Wed Oct 05 2005 - 11:35:25 CDT)
- Re: ABF Simulation Chris Chipot (Wed Oct 05 2005 - 07:58:57 CDT)
- NAMD: error messages Sergio Anis (Tue Oct 04 2005 - 06:21:31 CDT)
- Is there a method to choose what is saved in DCD files xiaojing gong (Sun Oct 02 2005 - 09:34:02 CDT)
- Fedora Core 4 problems [2] ... Nicholas M Glykos (Sat Oct 01 2005 - 08:42:21 CDT)
- Fedora Core 4 problems (?) ... Nicholas M Glykos (Sat Oct 01 2005 - 08:08:55 CDT)
- namd 2.6b1 job crash error dimka (Fri Sep 30 2005 - 16:18:43 CDT)
- water box and system charge snoze pa (Fri Sep 30 2005 - 11:44:21 CDT)
- NAMD cluster run snoze pa (Fri Sep 30 2005 - 10:35:22 CDT)
- Ca++ topology¶m files mustapha.hamdi_at_ensi-bourges.fr (Fri Sep 30 2005 - 04:11:31 CDT)
- pairInteraction energies? Georgios Papadopoulos (Fri Sep 30 2005 - 01:32:46 CDT)
- error parsing config file dora guzman (Thu Sep 29 2005 - 14:00:00 CDT)
- unexpected end with NAMD on quad-dual core opteron machine JIMENEZ Ralph (Thu Sep 29 2005 - 12:59:42 CDT)
- problems NAMD_2.6 (fwd) carles ferrer (Thu Sep 29 2005 - 04:06:09 CDT)
- NAMD on SUN floquet_at_icsn.cnrs-gif.fr (Thu Sep 29 2005 - 01:31:03 CDT)
- NAMD for Xeon clusters Xiongce Zhao (Wed Sep 28 2005 - 17:13:06 CDT)
- About Potential Addition in NAMD yangbing00_at_mails.tsinghua.edu.cn (Wed Sep 28 2005 - 06:45:18 CDT)
- About ions Representation in NAMD yangbing00_at_mails.tsinghua.edu.cn (Wed Sep 28 2005 - 06:40:45 CDT)
- Using an arbitrary tabulated potential in NAMD Joshua D. Moore (Tue Sep 27 2005 - 21:44:26 CDT)
- random seed ioana_at_pegasus.arc.nasa.gov (Tue Sep 27 2005 - 20:14:25 CDT)
- NAMD running problem Jason Lee (Tue Sep 27 2005 - 15:02:27 CDT)
- SHAKE or not? Gianluca Interlandi (Tue Sep 27 2005 - 14:42:43 CDT)
- Another question about MD simulation of a domain. Boyang Wang (Tue Sep 27 2005 - 12:30:43 CDT)
- A question about MD simulation of peptide. Boyang Wang (Tue Sep 27 2005 - 12:24:59 CDT)
- calculate enthalpy of binding Georgios Papadopoulos (Tue Sep 27 2005 - 11:33:33 CDT)
- ptraj Michel Espinoza-Fonseca (Tue Sep 27 2005 - 06:24:50 CDT)
- Re: hi all, I want to know how to turn the debug mode on of the namd q=E2=BA=E9=C3=F7?= (Mon Sep 26 2005 - 23:43:25 CDT)
- It is posible to allow Bond and angle degrees of freedom in tip3 water?? Leonardo Sepulveda Durán (Mon Sep 26 2005 - 16:52:55 CDT)
- RE: Constraint failure Michel Espinoza-Fonseca (Mon Sep 26 2005 - 13:54:52 CDT)
- Constraint failure Po Hu (Sat Sep 24 2005 - 13:42:42 CDT)
- hi all, I want to know how to turn the debug mode on of the namd q=E2=BA=E9=C3=F7?= (Mon Sep 26 2005 - 09:56:17 CDT)
- temperature coupling and pressure coupling xiaojing gong (Mon Sep 26 2005 - 01:44:16 CDT)
- energy minimization xiaojing gong (Sun Sep 25 2005 - 22:05:32 CDT)
- energy minimization xiaojing gong (Sun Sep 25 2005 - 21:57:00 CDT)
- Re: rotating constraints Anna Modzelewska (Wed Sep 21 2005 - 04:22:30 CDT)
- RE: autoionize & namd2 Michel Espinoza-Fonseca (Wed Sep 21 2005 - 02:24:09 CDT)
- Fix distance Ekta Khurana (Tue Sep 20 2005 - 18:11:06 CDT)
- autoionize & namd2 bo baker (Tue Sep 20 2005 - 18:07:34 CDT)
- reconstructing backbone with psfgen Michel Espinoza-Fonseca (Tue Sep 20 2005 - 09:07:04 CDT)
- reconstructing backbone with psfgen Michel Espinoza-Fonseca (Tue Sep 20 2005 - 05:45:10 CDT)
- How to use AMBER force field in NAMD? Po Hu (Mon Sep 19 2005 - 20:31:13 CDT)
- Re: log file bo baker (Mon Sep 19 2005 - 16:55:33 CDT)
- segmentation fault on Linux dimka (Mon Sep 19 2005 - 16:48:02 CDT)
- Re: segmentation fault on Linux dimka (Mon Nov 28 2005 - 12:41:25 CST)
- pair.pdb and cutoff for pairInteraction Shirley Li (Tue Nov 29 2005 - 11:00:02 CST)
- Re: pair.pdb and cutoff for pairInteraction Peter Freddolino (Tue Nov 29 2005 - 11:26:19 CST)
- Re: pair.pdb and cutoff for pairInteraction Shirley Li (Tue Nov 29 2005 - 22:33:36 CST)
- Re: pair.pdb and cutoff for pairInteraction JC Gumbart (Tue Nov 29 2005 - 23:52:51 CST)
- Re: pair.pdb and cutoff for pairInteraction JC Gumbart (Wed Nov 30 2005 - 00:10:44 CST)
- pair.pdb and cutoff for pairInteraction Shirley Li (Tue Nov 29 2005 - 11:00:02 CST)
- Re: segmentation fault on Linux dimka (Mon Nov 28 2005 - 12:41:25 CST)
- log file bo baker (Mon Sep 19 2005 - 14:09:42 CDT)
- "Segmentation violation" on running namd2.6b1 Dong Luo (Mon Sep 19 2005 - 10:36:30 CDT)
- Binding Energies for a Peptide-RNA System rossi_at_york.cuny.edu (Sat Sep 17 2005 - 14:37:11 CDT)
- NAMD2.6b1 (&2.5) binaries on Scyld (missing libbproc.so.2 lib?) Nicolae-Viorel Buchete (Thu Sep 15 2005 - 16:44:28 CDT)
- Partial charges for fluorescein/topology file Shahid Qamar (Thu Sep 15 2005 - 13:19:41 CDT)
- PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP Troy Wymore (Thu Sep 15 2005 - 11:22:29 CDT)
- problem while running NAMD Imran Khan (Wed Sep 14 2005 - 11:25:56 CDT)
- energy values Anna Modzelewska (Tue Sep 13 2005 - 06:29:27 CDT)
- namd performance on altix machines Michel Espinoza-Fonseca (Fri Sep 09 2005 - 07:10:48 CDT)
- Free Energy of Conformational Change Calculations Error: "Problem parsing input parameters Error: Invalid AtomID" Joshua D. Moore (Thu Sep 08 2005 - 22:13:17 CDT)
- surface density of lipid bilayer Gan, Yong \(UMC-Student\) (Thu Sep 08 2005 - 12:42:21 CDT)
- namd2.6b1 hang on IBM p-690 Dong Luo (Thu Sep 08 2005 - 10:50:21 CDT)
- RE: Sybyl trajectory Edelmiro Moman (Tue Sep 06 2005 - 10:33:37 CDT)
- vmd-l: script Sergio Anis (Tue Sep 06 2005 - 07:11:50 CDT)
- Re: vmd-l: Sybyl trajectory Josef Scheiber (Tue Sep 06 2005 - 05:38:38 CDT)
- Ammasso interconnect performance, LDB question Dow Hurst (Mon Sep 05 2005 - 23:21:12 CDT)
- Sybyl trajectory Josef Scheiber (Mon Sep 05 2005 - 01:56:04 CDT)
- abf michael atkinson (Sun Sep 04 2005 - 22:21:29 CDT)
- vmdtext and .cshrc. bo baker (Fri Sep 02 2005 - 18:26:29 CDT)
- Problem in restarting simulation Pijush Ghosh (Fri Sep 02 2005 - 10:54:54 CDT)
- NAMD running only at 40-50% CPU capacity LEWYN LI (Fri Sep 02 2005 - 11:00:35 CDT)
- NAMD & Gromacs FF Mauricio Carrillo Tripp (Thu Sep 01 2005 - 16:21:50 CDT)
- wallclock and cputime Marc Q. Ma (Thu Sep 01 2005 - 16:31:01 CDT)
- Calculating forces Gaurav Sharma (Thu Sep 01 2005 - 12:32:59 CDT)
- vectorized NAMD version? Grzegorz Jezierski (Thu Sep 01 2005 - 09:42:35 CDT)
- pair interactions in NPT Anna Modzelewska (Thu Sep 01 2005 - 03:21:46 CDT)
- Can NAMD deal with solid-state system? weikai (Wed Aug 31 2005 - 21:57:21 CDT)
- NAMD 2.6b1 Skipped Writing Velocity Restart File Joshua D. Moore (Tue Aug 30 2005 - 01:09:20 CDT)
- problem when heating the system Phoenix (Mon Aug 29 2005 - 23:07:42 CDT)
- dramatical standard deviation in the pressure profile Nicolas Sapay (Mon Aug 29 2005 - 07:12:27 CDT)
- NPT and FIXED atoms Sascha Tayefeh (Mon Aug 29 2005 - 02:14:28 CDT)
- NAMD on PSC Gan, Yong \(UMC-Student\) (Sun Aug 28 2005 - 12:26:30 CDT)
- creating a pdb file based on sequence and psi phi omega values only Matan Dishon (Sun Aug 28 2005 - 04:58:07 CDT)
- Pressure Profile Simulation Gan, Yong \(UMC-Student\) (Wed Aug 24 2005 - 21:36:51 CDT)
- Crash during free energy calculation (MCTI) Grzegorz Jezierski (Wed Aug 24 2005 - 02:47:07 CDT)
- NAMD2.6b1 on an OSX cluster Michael Grabe (Tue Aug 23 2005 - 17:16:56 CDT)
- Extra terms in the expression for potential energy Grzegorz Jezierski (Tue Aug 23 2005 - 12:04:35 CDT)
- About the command "loadtotalforces" LEWYN LI (Mon Aug 22 2005 - 21:25:44 CDT)
- peptide out of the water-box Navratna Vajpai (Mon Aug 22 2005 - 02:52:11 CDT)
- NBFix command to apply Lorentz-Berthelot mixing rules Joshua D. Moore (Sun Aug 21 2005 - 14:45:59 CDT)
- problem when do equilibration ÎâºéÃ÷ (Sun Aug 21 2005 - 03:40:44 CDT)
- Compiling charm++-5.9: Problems with g++ Gianluca Interlandi (Sat Aug 20 2005 - 05:36:26 CDT)
- Fatal error on PE 0> FATAL ERROR: DIHEDRALS INDEX 150255520 Brian Bennion (Fri Aug 19 2005 - 16:47:19 CDT)
- NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers Rene Salmon (Fri Aug 19 2005 - 10:38:20 CDT)
- Re: Large Box Sizes and Total Energies Observed in NAMD 2.6b1 Binaries of AIX-POWER-MPI and Origin2000-MPI Joshua D. Moore (Fri Aug 19 2005 - 06:38:04 CDT)
- Large Box Sizes and Total Energies Observed in NAMD 2.6b1 Binaries of AIX-POWER-MPI and Origin2000-MPI Joshua D. Moore (Thu Aug 18 2005 - 17:35:21 CDT)
- par_all27_prot_lipid.inp bo baker (Thu Aug 18 2005 - 16:29:15 CDT)
- Linux-MPI binary of NAMD 2.6b1 Joshua D. Moore (Thu Aug 18 2005 - 06:09:41 CDT)
- moments of inertia, principal axes Stern, Julie (Wed Aug 17 2005 - 19:00:53 CDT)
- undefined symbol errors:__builtin_bzero and _alloca building mpi-ppc-darwin version of namd2.6b1 Jerry Ebalunode (Wed Aug 17 2005 - 13:58:40 CDT)
- New BioCoRE server released Robert Brunner (Wed Aug 17 2005 - 12:00:16 CDT)
- scripts for binding free energy calculation using SMD and Jarzynski's equality Marc Q. Ma (Wed Aug 17 2005 - 09:45:12 CDT)
- Compilation of NAMD on 64-bit NUMA Imran Khan (Wed Aug 17 2005 - 04:58:23 CDT)
- Re: errno = 2 bo baker (Tue Aug 16 2005 - 19:04:49 CDT)
- PSF file generation Tamal Banerjee (Tue Aug 16 2005 - 00:16:46 CDT)
- errno = 2 bo baker (Mon Aug 15 2005 - 19:05:21 CDT)
- Manipulating structure Mikolai Fajer (Mon Aug 15 2005 - 09:57:03 CDT)
- problem about equilibration xiaojing gong (Mon Aug 15 2005 - 08:30:44 CDT)
- namd 6-1- abf michael atkinson (Mon Aug 15 2005 - 01:38:36 CDT)
- Psfgen within NAMD Mikolai Fajer (Fri Aug 12 2005 - 12:01:37 CDT)
- (no subject) Giovanni Bellesia (Thu Aug 11 2005 - 15:50:38 CDT)
- rescaling of coordinates in PBC simulations Giovanni Bellesia (Thu Aug 11 2005 - 12:41:52 CDT)
- How to "extract" coordinates from a DCD trajectory file? Edelmiro Moman (Tue Aug 09 2005 - 07:10:00 CDT)
- namd hangs Uma Mahankali (Mon Aug 08 2005 - 23:10:13 CDT)
- Charmm++5.9 build on Mac OS X by IB xlc compiler Jason Lee (Mon Aug 08 2005 - 14:58:21 CDT)
- Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Gengbin Zheng (Tue Aug 09 2005 - 11:59:15 CDT)
- RE: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Jason Lee (Tue Aug 30 2005 - 18:04:43 CDT)
- Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Gengbin Zheng (Wed Aug 31 2005 - 12:32:56 CDT)
- Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Gengbin Zheng (Wed Aug 31 2005 - 14:18:07 CDT)
- Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Jason Lee (Thu Sep 01 2005 - 16:46:24 CDT)
- Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Gengbin Zheng (Fri Sep 02 2005 - 00:34:03 CDT)
- Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Jason Lee (Fri Sep 02 2005 - 10:55:13 CDT)
- Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Gengbin Zheng (Sun Sep 04 2005 - 11:08:03 CDT)
- RE: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Jason Lee (Tue Aug 30 2005 - 18:04:43 CDT)
- Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Gengbin Zheng (Tue Aug 09 2005 - 11:59:15 CDT)
- add ions Mahalakshmi Sahasranaman (Mon Aug 08 2005 - 07:41:33 CDT)
- Periodic boundary conditions Navratna Vajpai (Mon Aug 08 2005 - 03:34:34 CDT)
- For help with .log file. Boyang Wang (Sun Aug 07 2005 - 14:13:33 CDT)
- 4th Annual Workshop on Charm++ and its Applications 2005 Jim Phillips (Fri Aug 05 2005 - 17:40:30 CDT)
- volume from VMD and NAMD different? Brian Bennion (Fri Aug 05 2005 - 16:12:34 CDT)
- error in config file Brian Bennion (Fri Aug 05 2005 - 11:28:14 CDT)
- Fatal error: vivek sharma (Thu Aug 04 2005 - 07:58:30 CDT)
- wrap ions Stern, Julie (Wed Aug 03 2005 - 23:13:05 CDT)
- Help with psf and par for small molecules santanu chatterjee (Wed Aug 03 2005 - 15:12:40 CDT)
- shake and minimzation, equilibration Stern, Julie (Wed Aug 03 2005 - 14:56:13 CDT)
- rigidBond water Stern, Julie (Wed Aug 03 2005 - 13:45:07 CDT)
- ERROR: Margin is too small (BUG?) Mauricio Carrillo Tripp (Wed Aug 03 2005 - 10:02:42 CDT)
- velocity quenching Stern, Julie (Tue Aug 02 2005 - 23:15:45 CDT)
- steepest descent minimization Stern, Julie (Tue Aug 02 2005 - 22:35:00 CDT)
- Running NAMD on a multiprocessor computer Gan, Yong \(UMC-Student\) (Tue Aug 02 2005 - 19:00:05 CDT)
- charm++ 5.9 megatest failure too Dow_Hurst (Tue Aug 02 2005 - 17:25:38 CDT)
- charm++ 5.9 build fails, NAMD 2.6b1 make fails Dow_Hurst (Tue Aug 02 2005 - 17:16:55 CDT)
- 2.6b1 source missing file Dow_Hurst (Tue Aug 02 2005 - 16:58:30 CDT)
- learning how to do a Cys palmitoyl patch seigneuret_at_cochin.inserm.fr (Tue Aug 02 2005 - 16:24:19 CDT)
- Link Ammasso MPI with NAMD Dow_Hurst (Tue Aug 02 2005 - 14:46:59 CDT)
- Link Ammasso MPI with NAMD Dow_Hurst (Tue Aug 02 2005 - 14:43:17 CDT)
- RE: Nanotube Simulations Michel Espinoza-Fonseca (Tue Aug 02 2005 - 09:50:18 CDT)
- Nanotube Simulations Gaurav Sharma (Tue Aug 02 2005 - 08:51:14 CDT)
- LDB question Jason Lee (Mon Aug 01 2005 - 21:06:19 CDT)
- H-H bond in TIP3 water Jorge Pikunic (Mon Aug 01 2005 - 17:21:26 CDT)
- running on two different machines.... Navratna Vajpai (Sun Jul 31 2005 - 02:24:39 CDT)
- error running namd 13200178 Hendra Tampang Allo (Mon Aug 01 2005 - 04:39:38 CDT)
- running on two different machines.... Navratna Vajpai (Sun Jul 31 2005 - 02:27:57 CDT)
- problem using visual_mdenergy: program has trouble reading the dat file patrick wintrode (Sat Jul 30 2005 - 17:08:45 CDT)
- Re: Report on a trajectory incompatibility between NAMD and CHARMM: Unfolding and RDFs NAVEEN P MICHAUD AGRAWAL (Sat Jul 30 2005 - 10:42:29 CDT)
- H-H bond in solvate Jorge Pikunic (Sat Jul 30 2005 - 08:57:59 CDT)
- how to use the dual-processor machines Xiaoqing Wang (Sat Jul 30 2005 - 08:37:39 CDT)
- constraint constant in equilibration xiaojing gong (Sat Jul 30 2005 - 00:19:26 CDT)
- NAMD 2.6b1 Released Jim Phillips (Fri Jul 29 2005 - 18:55:59 CDT)
- Report on a trajectory incompatibility between NAMD and CHARMM: Unfolding and RDFs Mauricio Carrillo Tripp (Fri Jul 29 2005 - 16:36:07 CDT)
- RE: shape change of water box and peptide move out Michel Espinoza-Fonseca (Fri Jul 29 2005 - 12:35:09 CDT)
- shape change of water box and peptide move out Dong Luo (Fri Jul 29 2005 - 12:09:58 CDT)
- ATP in the Topology file Pedro Borkowski (Fri Jul 29 2005 - 11:31:27 CDT)
- opteron 64bit installation Kyle Gustafson (Fri Jul 29 2005 - 10:29:11 CDT)
- Parameter files for Nanotube Simulation Gaurav Sharma (Thu Jul 28 2005 - 16:26:49 CDT)
- restarting SMD jobs Vani Krishna (Tue Jul 26 2005 - 20:25:38 CDT)
- VMD solvate in CCl4 Jack (Tue Jul 26 2005 - 08:37:08 CDT)
- Class I vs Class II force fields Aaron Oakley (Tue Jul 26 2005 - 00:42:01 CDT)
- compiling NAMD: plugins Kyle Gustafson (Mon Jul 25 2005 - 19:53:01 CDT)
- Re: mpi problems on opteron Kyle Gustafson (Mon Jul 25 2005 - 19:04:56 CDT)
- mpi problems on opteron Kyle Gustafson (Mon Jul 25 2005 - 16:05:02 CDT)
- NAMD on dual opterons Kyle Gustafson (Mon Jul 25 2005 - 13:30:44 CDT)
- fep file Deborah Jameson (Mon Jul 25 2005 - 11:10:54 CDT)
- CCS ERROR during simulation Jason Lee (Mon Jul 25 2005 - 08:52:16 CDT)
- Incorrect periodic box imaging with AMBER parameters Grzegorz Jezierski (Mon Jul 25 2005 - 04:11:20 CDT)
- Re: Incorrect periodic box imaging with AMBER parameters Charles Danko (Mon Jul 25 2005 - 08:32:20 CDT)
- Re: Incorrect periodic box imaging with AMBER parameters Grzegorz Jezierski (Thu Aug 04 2005 - 13:04:05 CDT)
- Re: Incorrect periodic box imaging with AMBER parameters surendra negi (Thu Aug 04 2005 - 16:11:15 CDT)
- Re: Incorrect periodic box imaging with AMBER parameters nordgren_at_sas.upenn.edu (Thu Aug 04 2005 - 17:40:58 CDT)
- Re: Incorrect periodic box imaging with AMBER parameters Grzegorz Jezierski (Fri Aug 05 2005 - 06:23:57 CDT)
- Re: Incorrect periodic box imaging with AMBER parameters Grzegorz Jezierski (Thu Aug 04 2005 - 13:04:05 CDT)
- Re: Incorrect periodic box imaging with AMBER parameters Grzegorz Jezierski (Mon Aug 08 2005 - 12:43:20 CDT)
- Re: Incorrect periodic box imaging with AMBER parameters Charles Danko (Mon Jul 25 2005 - 08:32:20 CDT)
- system becomes very large when set LangevinPiston on Xiaoqing Wang (Sun Jul 24 2005 - 22:06:43 CDT)
- Re: system becomes very large when set LangevinPiston on Xiaoqing Wang (Tue Jul 26 2005 - 04:48:13 CDT)
- the difference between the min_nacl.vel and min_nacl.restart.vel xiaojing gong (Sat Jul 23 2005 - 07:59:48 CDT)
- Fixed atoms and dcd file with DCDunitCell on Joshua D. Moore (Fri Jul 22 2005 - 16:46:15 CDT)
- output in tcl samantha cox (Fri Jul 22 2005 - 15:06:06 CDT)
- TM protein in octane slab questions Michel Seigneuret (Fri Jul 22 2005 - 03:52:50 CDT)
- added more bases to DNA using psfgen Stern, Julie (Thu Jul 21 2005 - 21:50:55 CDT)
- namdplot error Stern, Julie (Thu Jul 21 2005 - 20:06:53 CDT)
- catdcd-generated files and CHARMM Chang, Christopher (Thu Jul 21 2005 - 11:55:25 CDT)
- constrain or fix the system only in Z direction xiaojing gong (Thu Jul 21 2005 - 07:01:33 CDT)
- Energy Problem (Order of Magnitude) s.bora erdemli (Wed Jul 20 2005 - 15:05:03 CDT)
- removing water from DCD Stern, Julie (Wed Jul 20 2005 - 19:49:12 CDT)
- Re: removing water from DCD Shirley Hui (Wed Jul 20 2005 - 20:25:51 CDT)
- Re: removing water from DCD JC Gumbart (Wed Jul 20 2005 - 20:50:49 CDT)
- Re: removing water from DCD s.bora erdemli (Wed Jul 20 2005 - 21:06:53 CDT)
- Re: removing water from DCD Alessandro Pedretti (Thu Jul 21 2005 - 01:55:34 CDT)
- RE: removing water from DCD Pijush Ghosh (Wed Jul 20 2005 - 22:03:20 CDT)
- How to run for periodic boundary Conditions? Snigdha Chakraborty (Wed Jul 20 2005 - 12:19:32 CDT)
- Help with SMD Eunice Ramirez Melendez (Tue Jul 19 2005 - 12:08:34 CDT)
- hbonds output!!! Eunice Ramirez Melendez (Tue Jul 19 2005 - 11:59:30 CDT)
- Re: Ca trace only Sergio Anis (Wed Jul 20 2005 - 06:52:05 CDT)
- changing file Deborah Jameson (Wed Jul 20 2005 - 03:18:12 CDT)
- Bromine Matthew Wilce (Wed Jul 20 2005 - 01:43:43 CDT)
- cellBasisVectors and xsc files Stern, Julie (Tue Jul 19 2005 - 20:53:01 CDT)
- force shifted cutoff Stern, Julie (Tue Jul 19 2005 - 18:37:10 CDT)
- Ca trace only Shirley Hui (Tue Jul 19 2005 - 18:37:11 CDT)
- RE: Velocity after heating wmsmith (Mon Jul 18 2005 - 13:04:14 CDT)
- setting configuration file for free energy perturbation Deborah Jameson (Mon Jul 18 2005 - 10:25:02 CDT)
- Velocity after heating mustapha.hamdi_at_ensi-bourges.fr (Mon Jul 18 2005 - 06:56:03 CDT)
- pressure control in config file xiaojing gong (Sun Jul 17 2005 - 20:06:16 CDT)
- It appears that the Claim that NAMD works with gromacs is false Jim Kress (Sat Jul 16 2005 - 19:43:42 CDT)
- Re: fep Chris Chipot (Sat Jul 16 2005 - 04:48:02 CDT)
- FEP alchemical Amir Shamloo (Fri Jul 15 2005 - 19:51:23 CDT)
- psfgen and poorly guessed coordinates Stern, Julie (Fri Jul 15 2005 - 18:17:56 CDT)
- Runnig same config file many times Shahid Qamar (Fri Jul 15 2005 - 14:38:38 CDT)
- patch failed Hidekazu WATANABE (Fri Jul 15 2005 - 05:19:19 CDT)
- Random forces in Langevin temperature control -- three questions Blake Charlebois (Fri Jul 15 2005 - 00:05:03 CDT)
- patch PYRT and extending DNA Stern, Julie (Thu Jul 14 2005 - 20:17:04 CDT)
- psfgen and extending 5' end of DNA Stern, Julie (Thu Jul 14 2005 - 17:07:23 CDT)
- psfgen patches Stern, Julie (Thu Jul 14 2005 - 17:04:51 CDT)
- PDB files for carbon nanotubes Gaurav Sharma (Thu Jul 14 2005 - 14:33:05 CDT)
- sync buffer overflow Brian Bennion (Wed Jul 13 2005 - 16:44:36 CDT)
- MDenergy error floquet_at_icsn.cnrs-gif.fr (Wed Jul 13 2005 - 14:43:15 CDT)
- FATAL ERROR: child atom 39 bonded only to child H atoms Boyang Wang (Wed Jul 13 2005 - 11:06:19 CDT)
- Mother atom with hydrogenGroupSize of 0 Boyang Wang (Mon Jul 11 2005 - 17:57:51 CDT)
- Energy Order of Magnitude s.bora erdemli (Mon Jul 11 2005 - 11:20:15 CDT)
- RE: pka calculations and their use in simulations Michel Espinoza-Fonseca (Mon Jul 11 2005 - 07:41:49 CDT)
- pka calculations and their use in simulations Richard Law (Sun Jul 10 2005 - 18:12:00 CDT)
- NAMD/iAPBS Jerry Parks (Fri Jul 08 2005 - 16:19:15 CDT)
- SPC/E Water Model and RigidBonds Joshua D. Moore (Fri Jul 08 2005 - 15:46:41 CDT)
- xplor parameter to charmm ËïæÃæà (Fri Jul 08 2005 - 03:54:19 CDT)
- force shifted cutoff Stern, Julie (Thu Jul 07 2005 - 18:06:15 CDT)
- XPLOR psf format Stern, Julie (Thu Jul 07 2005 - 14:16:48 CDT)
- Van Der Waals energy sabri bora erdemli (Thu Jul 07 2005 - 09:07:44 CDT)
- van der waals energy SABRI BORA ERDEMLI (Thu Jul 07 2005 - 09:25:45 CDT)
- infinite DNA Stern, Julie (Wed Jul 06 2005 - 11:52:17 CDT)
- RE: Some questions about TCL wmsmith (Tue Jul 05 2005 - 17:20:54 CDT)
- Some questions about TCL Shahid Qamar (Tue Jul 05 2005 - 16:38:28 CDT)
- problems with autoionize total charge and minimization Leonardo Sepulveda Durán (Tue Jul 05 2005 - 14:18:25 CDT)
- dmpc membrane Swarna Patra (Mon Jul 04 2005 - 20:17:43 CDT)
- Re: Unable to Generate PSF file ! JC Gumbart (Mon Jul 04 2005 - 14:01:14 CDT)
- Unable to Generate PSF file ! Tamal Banerjee (Mon Jul 04 2005 - 08:09:43 CDT)
- FEP - one long simulation vs many short ones Floris Buelens (Fri Jul 01 2005 - 07:07:14 CDT)
- MD stops when COM or atom reaches a distance Shahid Qamar (Fri Jul 01 2005 - 11:34:39 CDT)
- Segmentation fault with two processors floquet_at_icsn.cnrs-gif.fr (Fri Jul 01 2005 - 04:12:57 CDT)
- RE: [Scalex86 - linux] FW: segfaults in mm_malloc Tim Sirianni (Thu Jun 30 2005 - 18:20:44 CDT)
- How MD stopes at a specific distance? Shahid Qamar (Thu Jun 30 2005 - 12:41:54 CDT)
- psfgen/auto none vivek sharma (Thu Jun 30 2005 - 02:50:30 CDT)
- removing a covalent bond during a simulation patrick wintrode (Wed Jun 29 2005 - 12:10:56 CDT)
- Segment atom number limitation Jason Lee (Wed Jun 29 2005 - 11:18:50 CDT)
- Re: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) Sascha Tayefeh (Wed Jun 29 2005 - 09:56:54 CDT)
- Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) Sascha Tayefeh (Wed Jun 29 2005 - 09:31:23 CDT)
- Re: interactions in flexible cel Anna Modzelewska (Wed Jun 29 2005 - 02:07:04 CDT)
- interactions in flexible cel Anna Modzelewska (Wed Jun 29 2005 - 00:34:51 CDT)
- convert_from_namd_to_amber Wei Chen (Tue Jun 28 2005 - 22:02:18 CDT)
- free energy pertubation,binding energy and constant s.bora erdemli (Tue Jun 28 2005 - 14:30:07 CDT)
- segfaults in mm_malloc Brian Bennion (Tue Jun 28 2005 - 10:27:31 CDT)
- Periodic Boundary Conditions and Wrap Joshua D. Moore (Tue Jun 28 2005 - 03:31:38 CDT)
- PMF force restraint question Leonardo Sepulveda Durán (Mon Jun 27 2005 - 19:11:11 CDT)
- cross products wmsmith (Mon Jun 27 2005 - 14:35:18 CDT)
- namdplot, grpah is empty Raeanne Napoleon (Mon Jun 27 2005 - 11:01:58 CDT)
- membrane protein md protocol rob yang (Mon Jun 27 2005 - 10:36:15 CDT)
- Accessing beta / occupancy values from NAMD tcl wmsmith (Mon Jun 27 2005 - 10:24:47 CDT)
- catdcd and dcdunitcell Philip Fowler (Mon Jun 27 2005 - 05:07:01 CDT)
- Re: catdcd and dcdunitcell Ben Roberts (Mon Jun 27 2005 - 07:47:39 CDT)
- Re: catdcd and dcdunitcell Philip Fowler (Tue Jun 28 2005 - 07:15:36 CDT)
- Re: catdcd and dcdunitcell Philip Fowler (Tue Jun 28 2005 - 07:18:15 CDT)
- Re: catdcd and dcdunitcell Jérôme Hénin (Tue Jun 28 2005 - 09:14:32 CDT)
- Re: catdcd and dcdunitcell Philip Fowler (Tue Jun 28 2005 - 09:27:06 CDT)
- Re: catdcd and dcdunitcell Jérôme Hénin (Tue Jun 28 2005 - 10:54:09 CDT)
- Re: catdcd and dcdunitcell Philip Fowler (Tue Jun 28 2005 - 11:07:38 CDT)
- Re: catdcd and dcdunitcell Ben Roberts (Tue Jun 28 2005 - 18:27:07 CDT)
- Re: catdcd and dcdunitcell Joshua D. Moore (Fri Jul 22 2005 - 16:04:00 CDT)
- Re: catdcd and dcdunitcell Ben Roberts (Mon Jun 27 2005 - 07:47:39 CDT)
- peptide simulation Matan Dishon (Mon Jun 27 2005 - 03:28:18 CDT)
- Using FEP as non-disruptive mutation procedure Leonardo Sepulveda Durán (Sun Jun 26 2005 - 17:10:17 CDT)
- new approach to counter FEP end-point VDW clashes Floris Buelens (Sun Jun 26 2005 - 07:41:14 CDT)
- changuing dihedral angle slowly (complete message) Leonardo Sepulveda Durán (Fri Jun 24 2005 - 17:47:02 CDT)
- changuing dihedral angle slowly Leonardo Sepulveda Durán (Fri Jun 24 2005 - 17:35:20 CDT)
- interactions in flexible cell Anna Modzelewska (Fri Jun 24 2005 - 04:31:27 CDT)
- Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS Phoenix (Fri Jun 24 2005 - 00:08:37 CDT)
- how to build AQP1 tetramer xiaojing gong (Thu Jun 23 2005 - 21:31:13 CDT)
- basic: combining two pdb files? Meunier, Vincent (Thu Jun 23 2005 - 20:16:45 CDT)
- Zeros at the beginning of each line in the output Joshua D. Moore (Thu Jun 23 2005 - 19:17:43 CDT)
- hard wall Mauricio Carrillo Tripp (Thu Jun 23 2005 - 11:24:00 CDT)
- electron density profiles (EDP) akash.khandelwal_at_ndsu.edu (Wed Jun 22 2005 - 14:25:23 CDT)
- Z-origin set to zero by Linux/Mac 2.5 binaries, Minimisation shaila_at_biof.ufrj.br (Wed Jun 22 2005 - 07:01:14 CDT)
- Understanding NAMD performance data Niraj kumar (Wed Jun 22 2005 - 05:27:10 CDT)
- RE: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Joshua D. Moore (Wed Jun 22 2005 - 00:58:48 CDT)
- Fluorophors ? Georgios Papadopoulos (Wed Jun 22 2005 - 00:27:25 CDT)
- Fixed restraint Shahid Qamar (Tue Jun 21 2005 - 17:56:09 CDT)
- langevin vs coupling to a heat bath patrick wintrode (Tue Jun 21 2005 - 15:25:29 CDT)
- namdplot, graph is empty Raeanne Napoleon (Tue Jun 21 2005 - 13:48:34 CDT)
- restart syntax Mark A. Hallman (Tue Jun 21 2005 - 13:23:16 CDT)
- Gramicidin Swarna Patra (Mon Jun 20 2005 - 20:54:09 CDT)
- shmget error Gianluca Interlandi (Mon Jun 20 2005 - 07:46:28 CDT)
- autoimd on windows Anna Modzelewska (Mon Jun 20 2005 - 06:40:29 CDT)
- Error when running NAMD at SDSC Joshua D. Moore (Sun Jun 19 2005 - 22:13:20 CDT)
- Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Leonardo Sepulveda Durán (Sun Jun 19 2005 - 12:58:18 CDT)
- velocity file of atoms at each time step debashis.sikdar_at_ndsu.edu (Sun Jun 19 2005 - 22:28:14 CDT)
- Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Brian Bennion (Mon Jun 20 2005 - 10:26:49 CDT)
- Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Aaron Oakley (Tue Jun 21 2005 - 01:48:52 CDT)
- Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Brian Bennion (Tue Jun 21 2005 - 10:08:32 CDT)
- Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Leonardo Sepulveda Durán (Tue Jun 21 2005 - 12:42:07 CDT)
- Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Marc Q. Ma (Tue Jun 21 2005 - 14:11:43 CDT)
- RE: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Blake Charlebois (Tue Jun 21 2005 - 15:41:19 CDT)
- RE: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Brian Bennion (Tue Jun 21 2005 - 17:40:15 CDT)
- Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Brian Bennion (Tue Jun 21 2005 - 10:08:32 CDT)
- Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? apw397_at_soton.ac.uk (Wed Jun 22 2005 - 10:41:58 CDT)
- Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? apw397_at_soton.ac.uk (Wed Jun 22 2005 - 10:42:04 CDT)
- Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Marcos Sotomayor (Sun Jun 26 2005 - 14:04:28 CDT)
- optimisation for dual CPU sytem Floris Buelens (Sat Jun 18 2005 - 08:25:39 CDT)
- Pressure_control Wei Chen (Fri Jun 17 2005 - 21:41:19 CDT)
- binding free energy , binding constant sabri bora erdemli (Fri Jun 17 2005 - 08:11:33 CDT)
- Problem with mdenergy floquet_at_icsn.cnrs-gif.fr (Fri Jun 17 2005 - 08:05:41 CDT)
- set center Swarna Patra (Thu Jun 16 2005 - 22:53:28 CDT)
- aquaporin question Samuel Flores (Thu Jun 16 2005 - 15:39:11 CDT)
- Charmm 1,4 Interactions - Scaling Question Paul R Brenner (Thu Jun 16 2005 - 12:00:05 CDT)
- force calculation Manuela Cavallari (Thu Jun 16 2005 - 11:53:13 CDT)
- Radial Distribution Function Pijush Ghosh (Thu Jun 16 2005 - 10:43:18 CDT)
- How to conservate energy during NVE simulations??? Leonardo Sepulveda Durán (Wed Jun 15 2005 - 20:55:29 CDT)
- Tcl forces Manuela Cavallari (Thu Jun 16 2005 - 05:51:05 CDT)
- Fw: changing default directory in VMD? Shirley Hui (Wed Jun 15 2005 - 15:34:51 CDT)
- Poorly guessed coordinates Maria Lin (Tue Jun 14 2005 - 14:03:59 CDT)
- addforce Leandro Martínez (Tue Jun 14 2005 - 10:02:28 CDT)
- MM/PBSA Wei Chen (Mon Jun 13 2005 - 15:41:45 CDT)
- RE: Adjusting Density of waterbox used by solvate Wolbach, Jeffrey P \(WOLBACH\) (Mon Jun 13 2005 - 11:36:11 CDT)
- c-shell into NAMD configuration file Ioana Cozmuta (Mon Jun 13 2005 - 02:02:48 CDT)
- FEP and TI Matthew Wilce (Sun Jun 12 2005 - 22:42:05 CDT)
- FEP and solvent Matthew Wilce (Sun Jun 12 2005 - 22:35:32 CDT)
- Simulation terminating due to RATTLE constraint failure Shirley Hui (Sun Jun 12 2005 - 22:21:09 CDT)
- Adjusting Density of waterbox used by solvate Leonardo Sepulveda Durán (Sun Jun 12 2005 - 21:51:51 CDT)
- velocity unit Gan, Yong \(UMC-Student\) (Sun Jun 12 2005 - 21:49:52 CDT)
- plugins.tar.gz & charm_src.tar.gz !!! Georgios Papadopoulos (Sat Jun 11 2005 - 05:38:27 CDT)
- water density calculation Leonardo Sepulveda Durán (Fri Jun 10 2005 - 21:19:50 CDT)
- it is posible to do NVE simulations in NAMD??? Leonardo Sepulveda Durán (Fri Jun 10 2005 - 18:04:16 CDT)
- interface with external program Leandro Martínez (Fri Jun 10 2005 - 13:15:30 CDT)
- RESTARTING CONJUGATE GRADIENT ALGORITHM Jason Lee (Fri Jun 10 2005 - 10:18:33 CDT)
- Script for MD in a loop? Shahid Qamar (Fri Jun 10 2005 - 10:05:34 CDT)
- implicit solvent Wei Zhuang (Thu Jun 09 2005 - 17:47:48 CDT)
- FEP error: Rattle atom constriant Shahid Qamar (Thu Jun 09 2005 - 15:59:11 CDT)
- large vanderwalls energy during minimization shgnwgn_at_eden.rutgers.edu (Thu Jun 09 2005 - 13:31:53 CDT)
- Namd on Mac os X Maria Lin (Wed Jun 08 2005 - 18:57:10 CDT)
- Number of Steps Pijush Ghosh (Wed Jun 08 2005 - 13:39:34 CDT)
- Multiple Harmonic Constraints Sascha Tayefeh (Thu Jun 09 2005 - 02:31:38 CDT)
- multiple automated calls to NAMD nordgren_at_sas.upenn.edu (Wed Jun 08 2005 - 20:57:56 CDT)
- Reverse Free Energy perturbation (FEP)? Shahid Qamar (Wed Jun 08 2005 - 15:35:30 CDT)
- Namd hangs on Bproc cluster Rene Salmon (Wed Jun 08 2005 - 11:55:00 CDT)
- Avoiding Rotation and translation of protein Leonardo Sepulveda Durán (Wed Jun 08 2005 - 10:58:33 CDT)
- Re: Installing NAMD on beowulf cluster, 64 bit, opteron, 4 processors. Gengbin Zheng (Tue Jun 07 2005 - 13:58:15 CDT)
- config files Mark A. Hallman (Tue Jun 07 2005 - 12:17:35 CDT)
- NAMD on IBM pSeries (690, 655) Dong Luo (Tue Jun 07 2005 - 11:45:53 CDT)
- NAMD on fedora 3 core? Georgios Papadopoulos (Tue Jun 07 2005 - 01:33:49 CDT)
- Installing NAMD on beowulf cluster, 64 bit, opteron, 4 processors. Wang, Boyang (Mon Jun 06 2005 - 22:23:59 CDT)
- relating FEP-derived ddG values to experimental IC50 Floris Buelens (Mon Jun 06 2005 - 17:49:54 CDT)
- how to apply a random force on a atom q=E2=BA=E9=C3=F7?= (Mon Jun 06 2005 - 12:31:46 CDT)
- hi ,everyone.I have a problem about random force q=E2=BA=E9=C3=F7?= (Mon Jun 06 2005 - 11:48:08 CDT)
- inorganic surface peptide simulation Matan Dishon (Mon Jun 06 2005 - 07:13:07 CDT)
- rigidBonds water Joshua D. Moore (Sun Jun 05 2005 - 21:39:09 CDT)
- Fe2+ parameters? Georgios Papadopoulos (Sun Jun 05 2005 - 04:52:09 CDT)
- charmm parameters for PEG li jianguo (Sat Jun 04 2005 - 23:42:26 CDT)
- ligands in VMD Leonardo Sepulveda Durán (Wed Jun 01 2005 - 20:20:02 CDT)
- Periodic Boundary Condition Gan, Yong \(UMC-Student\) (Wed Jun 01 2005 - 16:56:41 CDT)
- Generating a lot of segments in proper order and selection around a center of mass Leonardo Sepulveda Durán (Wed Jun 01 2005 - 16:13:35 CDT)
- question about nonnbonded parameters Leonardo Sepulveda Durán (Tue May 31 2005 - 11:04:23 CDT)
- Problem with solvate and PSF files in CHARMM format Leonardo Sepulveda Durán (Mon May 30 2005 - 18:37:05 CDT)
- Nanotube simulation in water problem Jason Lee (Mon May 30 2005 - 09:30:12 CDT)
- FEP charge perturbation Floris Buelens (Sun May 29 2005 - 17:50:28 CDT)
- NAMD hangs Michael Grabe (Sun May 29 2005 - 15:53:09 CDT)
- the lastest version of NAMD source junwang (Sun May 29 2005 - 12:29:35 CDT)
- questions about anisotropic pressure coupling Frank Yong Jiang (Sat May 28 2005 - 10:34:45 CDT)
- libimf.so problems Brian Bennion (Fri May 27 2005 - 15:22:07 CDT)
- PSFGEN Wei Chen (Fri May 27 2005 - 15:10:30 CDT)
- Multiple dihedral multiplicity floquet_at_icsn.cnrs-gif.fr (Fri May 27 2005 - 08:09:14 CDT)
- about *.psf ËïæÃæà (Thu May 26 2005 - 23:59:07 CDT)
- Segmentation violation in NAMD ! Parag Adhangale (Thu May 26 2005 - 11:04:41 CDT)
- Re: Compilation of Charm++ on Linux opteron cluster with MPICH-GM installed Gengbin Zheng (Wed May 25 2005 - 23:05:47 CDT)
- namddat not working Leonardo Sepulveda Durán (Tue May 24 2005 - 16:34:24 CDT)
- how to use gromacs force field in NAMD? Frank Yong Jiang (Tue May 24 2005 - 15:50:05 CDT)
- Re: Re: Simulated Annealing Config Leonardo Sepulveda Durán (Tue May 24 2005 - 14:55:49 CDT)
- pressure Wei Chen (Mon May 23 2005 - 19:50:28 CDT)
- Compilation of NAMD on opteron cluster with myrinet junwang (Mon May 23 2005 - 19:44:41 CDT)
- Milestoning in NAMD Shahid Qamar (Wed May 18 2005 - 15:46:19 CDT)
- Error in running tutorial files Ragothaman Yennamalli (Wed May 18 2005 - 12:20:50 CDT)
- inconsistencies with amber force fields due to scnb and 1-4scalin g Stern, Julie (Wed May 18 2005 - 10:38:51 CDT)
- steered molecular dynamics docking WONG Hua (Wed May 18 2005 - 04:55:37 CDT)
- regenerating PSF file Cetin Baloglu (Wed May 18 2005 - 01:07:05 CDT)
- How to set a molecule to be rigid in NAMD? Boyang Wang (Mon May 16 2005 - 14:37:44 CDT)
- Tyrocine dynamics came out wrong. Boyang Wang (Sun May 15 2005 - 20:08:08 CDT)
- Re: Converting Gromacs OPLS parameters to Charmm format Joshua D. Moore (Tue May 17 2005 - 17:35:18 CDT)
- Condition for stopping MD sim. with NAMD Nicolas Floquet (Tue May 17 2005 - 02:56:45 CDT)
- "make" Linux-amd64-g++ error Xiaoqing Wang (Sun May 15 2005 - 22:31:47 CDT)
- What's wrong with my namd2 Xiaoqing Wang (Sun May 15 2005 - 07:01:13 CDT)
- Generating psf for a drug, trimethoprim Charles Moad (Sat May 14 2005 - 18:00:08 CDT)
- benzene in NAMD Boyang Wang (Sat May 14 2005 - 15:33:13 CDT)
- Trajectory file. Boyang Wang (Fri May 13 2005 - 16:20:17 CDT)
- Megatest fails on Linux cluster Sterling Paramore (Fri May 13 2005 - 14:40:11 CDT)
- namddat: Command not found Mikolai Fajer (Thu May 12 2005 - 12:41:46 CDT)
- dielectric constant Dong Luo (Thu May 12 2005 - 11:52:42 CDT)
- scnb scaling factor and compatibility with AMBER force fields Stern, Julie (Thu May 12 2005 - 11:47:01 CDT)
- Force constant of harmonic restraint picot.delphine_at_neuf.fr (Thu May 12 2005 - 03:50:11 CDT)
- libimf.so error when compiling charm++ Ben Roberts (Thu May 12 2005 - 01:09:36 CDT)
- Compliling NAMD in RedHat9 Karina Martinez (Wed May 11 2005 - 21:59:28 CDT)
- FEP Chris Chipot (Wed May 11 2005 - 17:34:47 CDT)
- FEP Wei Chen (Wed May 11 2005 - 13:49:53 CDT)
- Energy minimization mustapha.hamdi_at_ensi-bourges.fr (Wed May 11 2005 - 12:33:01 CDT)
- Energy minimization mustapha.hamdi_at_ensi-bourges.fr (Wed May 11 2005 - 09:46:40 CDT)
- non-repeatability NAMD simulations roberte_at_organ.su.se (Tue May 10 2005 - 17:08:30 CDT)
- Bad global exclusion count. Boyang Wang (Tue May 10 2005 - 11:56:32 CDT)
- different result from different cpu Xiaoqing Wang (Tue May 10 2005 - 07:31:31 CDT)
- compile "mpi" charm++ on amd64 Xiaoqing Wang (Mon May 09 2005 - 22:09:32 CDT)
- Minimization with NAMD valesrdp (Mon May 09 2005 - 09:17:57 CDT)
- NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Niraj kumar (Mon May 09 2005 - 06:03:19 CDT)
- Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Gengbin Zheng (Tue May 10 2005 - 01:45:25 CDT)
- Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Niraj kumar (Tue May 10 2005 - 04:48:59 CDT)
- NOE constraints with NAMD Gianluca Interlandi (Tue May 10 2005 - 09:25:35 CDT)
- Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Gengbin Zheng (Tue May 10 2005 - 09:57:04 CDT)
- Re: Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Niraj kumar (Wed May 11 2005 - 01:40:56 CDT)
- Re: Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Gengbin Zheng (Wed May 11 2005 - 22:07:13 CDT)
- Re: Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Niraj kumar (Mon May 16 2005 - 05:14:31 CDT)
- Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Niraj kumar (Tue May 10 2005 - 04:48:59 CDT)
- Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Gengbin Zheng (Tue May 10 2005 - 01:45:25 CDT)
- NAMD automation nordgren_at_sas.upenn.edu (Sat May 07 2005 - 23:39:16 CDT)
- Fixing atoms during simulation Uma Mahankali (Sat May 07 2005 - 19:33:49 CDT)
- Problems compiling NAMD on linux/clustermatic 5 roberte_at_organ.su.se (Sat May 07 2005 - 05:54:18 CDT)
- Space environment simulations Gaurav Sharma (Fri May 06 2005 - 13:36:40 CDT)
- Space environment simulations Gaurav Sharma (Fri May 06 2005 - 13:20:53 CDT)
- Re: error message surendra negi (Fri May 06 2005 - 10:22:55 CDT)
- Re: charmm paramter Boyang Wang (Thu May 05 2005 - 22:23:56 CDT)
- protein/DNA complexes Matthew Wilce (Fri May 06 2005 - 00:27:34 CDT)
- RE: About Restart Michel Espinoza-Fonseca (Thu May 05 2005 - 21:50:29 CDT)
- RE: Restartname Michel Espinoza-Fonseca (Thu May 05 2005 - 21:48:00 CDT)
- charmm paramter akash.khandelwal_at_ndsu.edu (Thu May 05 2005 - 20:57:34 CDT)
- Restartname Boyang Wang (Thu May 05 2005 - 19:19:26 CDT)
- About Restart Boyang Wang (Thu May 05 2005 - 18:50:52 CDT)
- Problem using the GROMACS force field ! Parag Adhangale (Thu May 05 2005 - 16:23:52 CDT)
- Re: HEME patch surendra negi (Thu May 05 2005 - 13:38:37 CDT)
- hanging at startup phase 0 Dong Luo (Thu May 05 2005 - 10:47:31 CDT)
- RE: About PDB file with fixed atom flags. Michel Espinoza-Fonseca (Wed May 04 2005 - 17:07:13 CDT)
- About PDB file with fixed atom flags. Hidekazu WATANABE (Wed May 04 2005 - 16:40:23 CDT)
- RE: NAMD: HEM residue Michel Espinoza-Fonseca (Wed May 04 2005 - 15:17:34 CDT)
- NAMD simulation: HEME surendra negi (Wed May 04 2005 - 15:16:58 CDT)
- NAMD: HEM residue surendra negi (Wed May 04 2005 - 14:56:58 CDT)
- How to change psf file in the half way of VMD simulation? Boyang Wang (Tue May 03 2005 - 21:48:23 CDT)
- namd2 compile linux-i686-mpi Bing Xiong (Tue May 03 2005 - 15:38:27 CDT)
- compiling NAMD on a redhat-pentium-dell workstation paul.dalhaimer_at_yale.edu (Tue May 03 2005 - 11:54:56 CDT)
- Minimization after a MD simulation valesrdp (Tue May 03 2005 - 04:48:14 CDT)
- Re: SMD-drifting of center of mass Boyang Wang (Sun May 01 2005 - 22:21:46 CDT)
- NADP topology Hemant Kushwaha (Mon May 02 2005 - 04:40:58 CDT)
- Dihedral and Improper, Nonbonded. Wang, Boyang (Sun May 01 2005 - 22:46:22 CDT)
- SMD-drifting of center of mass Ekta Khurana (Sun May 01 2005 - 16:47:19 CDT)
- Parameter file again. Boyang Wang (Sat Apr 30 2005 - 12:20:19 CDT)
- Fwd: Parameter file. Boyang Wang (Sat Apr 30 2005 - 12:15:45 CDT)
- Parameter file. Boyang Wang (Fri Apr 29 2005 - 23:20:52 CDT)
- Combine pdb and psf files Gan, Yong \(UMC-Student\) (Fri Apr 29 2005 - 16:04:23 CDT)
- Tcl interface--dynamically changing simulation parameters Philip Blood (Thu Apr 28 2005 - 17:19:42 CDT)
- Regulating density of water Pijush Ghosh (Thu Apr 28 2005 - 13:44:35 CDT)
- RE: Generate psf file of DMPC membrane Gan, Yong \(UMC-Student\) (Thu Apr 28 2005 - 11:58:02 CDT)
- solvate and write pdb, psf file. Boyang Wang (Wed Apr 27 2005 - 19:16:28 CDT)
- Generate psf file of DMPC membrane Gan, Yong \(UMC-Student\) (Wed Apr 27 2005 - 22:10:34 CDT)
- (no subject) Wei Chen (Wed Apr 27 2005 - 11:04:07 CDT)
- Molecular Dynamics or Langevin Dynamics sabri bora erdemli (Tue Apr 26 2005 - 11:21:00 CDT)
- Gradient tolerance--total or per atom? Chang, Christopher (Tue Apr 26 2005 - 11:46:07 CDT)
- NAMD and dual core Opterons, thoughts? Dow Hurst (Tue Apr 26 2005 - 11:36:02 CDT)
- NAMD job abnormally killed with PBS Nicolas Sapay (Tue Apr 26 2005 - 02:14:33 CDT)
- a target molecule in a water box. Wang, Boyang (Mon Apr 25 2005 - 21:12:02 CDT)
- unwrapping dcd trajectory Mauricio Carrillo Tripp (Mon Apr 25 2005 - 16:47:42 CDT)
- Ferric heme Eunice Ramirez (Mon Apr 25 2005 - 11:54:41 CDT)
- Heat Capacity & Relaxation Functions Cetin Baloglu (Mon Apr 25 2005 - 03:22:11 CDT)
- Setting target minimization gradient? Chang, Christopher (Fri Apr 22 2005 - 13:15:01 CDT)
- (no subject) valesrdp (Thu Apr 21 2005 - 03:54:58 CDT)
- Interactive Simulations, ligand size limits.... Luis Rosales (Tue Apr 19 2005 - 22:51:52 CDT)
- Re: vmd-l: Interactive Simulations, ligand size limits.... John Stone (Wed Apr 20 2005 - 16:12:20 CDT)
- Re: vmd-l: Interactive Simulations, ligand size limits.... Luis Rosales (Wed Apr 20 2005 - 18:19:58 CDT)
- Re: Re: vmd-l: Interactive Simulations, ligand size limits.... Luis Rosales (Wed Apr 20 2005 - 22:22:10 CDT)
- Re: Re: vmd-l: Interactive Simulations, ligand size limits.... Luis Rosales (Wed Apr 27 2005 - 21:29:51 CDT)
- Re: Re: vmd-l: Interactive Simulations, ligand size limits.... John Stone (Thu Apr 28 2005 - 10:08:17 CDT)
- Re: Re: vmd-l: Interactive Simulations, ligand size limits.... Brian Bennion (Thu Apr 28 2005 - 12:01:32 CDT)
- Re: Re: vmd-l: Interactive Simulations, ligand size limits.... John Stone (Thu Apr 28 2005 - 13:05:40 CDT)
- Re: Re: vmd-l: Interactive Simulations, ligand size limits.... Marc Baaden (Fri Apr 29 2005 - 04:01:27 CDT)
- Re: vmd-l: Interactive Simulations, ligand size limits.... John Stone (Wed Apr 20 2005 - 16:12:20 CDT)
- duplicated key CA in psfgen mustapha.hamdi_at_ensi-bourges.fr (Tue Apr 19 2005 - 12:49:33 CDT)
- protein interact with its image Shunzhou Wan (Tue Apr 19 2005 - 10:23:58 CDT)
- addforce Leandro Martínez (Tue Apr 19 2005 - 09:38:50 CDT)
- Topology for nano tubes Alex Vakhrouchev (Tue Apr 19 2005 - 06:59:04 CDT)
- concatenating two or more dcd files Jorge Pikunic (Mon Apr 18 2005 - 10:44:07 CDT)
- NANMD errors: PME, qsub E. Davis Oldham (Sat Apr 16 2005 - 12:37:37 CDT)
- RE: minimization problem Stern, Julie (Thu Apr 14 2005 - 15:26:04 CDT)
- minimization problem Stern, Julie (Thu Apr 14 2005 - 13:41:19 CDT)
- RE: about protonation of HIS in membrane protein Michel Espinoza-Fonseca (Wed Apr 13 2005 - 19:47:52 CDT)
- RE: ERROR: Constraint failure in RATTLE algorithm for atom 127! Michel Espinoza-Fonseca (Wed Apr 13 2005 - 16:20:53 CDT)
- ERROR: Constraint failure in RATTLE algorithm for atom 127! Shahid Qamar (Wed Apr 13 2005 - 14:20:16 CDT)
- RE: Periodic cell has become too small for original patch grid Michel Espinoza-Fonseca (Wed Apr 13 2005 - 11:32:17 CDT)
- unstable simulation with AMBER ff in AMBER! Lina Nilsson (Wed Apr 13 2005 - 04:05:36 CDT)
- about protonation of HIS in membrane protein Baoqiang Cao (Wed Apr 13 2005 - 09:21:08 CDT)
- Periodic cell has become too small for original patch grid Xiaoqing Wang (Wed Apr 13 2005 - 03:38:33 CDT)
- AMBER ff system has too high velocities in NAMD Lina Nilsson (Wed Apr 13 2005 - 03:16:45 CDT)
- RE: ELECT energy Michel Espinoza-Fonseca (Mon Apr 11 2005 - 16:18:10 CDT)
- ELECT energy Stern, Julie (Mon Apr 11 2005 - 14:37:57 CDT)
- bonding to image Glenn Johnson (Mon Apr 11 2005 - 13:56:33 CDT)
- distance restraints during a dynamic Nicolas Sapay (Mon Apr 11 2005 - 11:13:40 CDT)
- density calculation Swarna Patra (Sun Apr 10 2005 - 20:24:51 CDT)
- RE: error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C Michel Espinoza-Fonseca (Sat Apr 09 2005 - 15:41:45 CDT)
- error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C Baoqiang Cao (Sat Apr 09 2005 - 14:40:37 CDT)
- RE: Michel Espinoza-Fonseca (Fri Apr 08 2005 - 12:27:54 CDT)
- phosphoserine Michel Espinoza-Fonseca (Fri Apr 08 2005 - 12:18:35 CDT)
- (no subject) Michael Grabe (Fri Apr 08 2005 - 12:04:37 CDT)
- box size changes under anisotropic pressure coupling Philip Blood (Fri Apr 08 2005 - 11:14:40 CDT)
- RE: Membrane configuration file Michel Espinoza-Fonseca (Fri Apr 08 2005 - 11:21:28 CDT)
- Membrane configuration file Lechuga, Javier (Fri Apr 08 2005 - 10:24:01 CDT)
- any script to build membrane+protein+solvent? Baoqiang Cao (Fri Apr 08 2005 - 10:02:36 CDT)
- Different electrostatic and Van der Waals cutoff Peter Spijker (Fri Apr 08 2005 - 04:56:42 CDT)
- performance differences on 2.4 vs. 2.6 Linux kernels Matt Harrington (Thu Apr 07 2005 - 19:10:54 CDT)
- RE: modifying cut off Michel Espinoza-Fonseca (Thu Apr 07 2005 - 19:01:03 CDT)
- modifying cut off Michel Espinoza-Fonseca (Thu Apr 07 2005 - 18:30:23 CDT)
- temperature autocorrelation Glenn Johnson (Thu Apr 07 2005 - 17:39:28 CDT)
- NAMD Myrinet issue - Strange behavior Edward Patrick Obrien (Thu Apr 07 2005 - 12:04:31 CDT)
- Checkpoint on IRIX of namd 2.5 job not MPI enabled Dow_Hurst (Thu Apr 07 2005 - 09:40:55 CDT)
- Myrinet vs. Infiniband wzhuang_at_uci.edu (Wed Apr 06 2005 - 12:36:10 CDT)
- RE: Nanotube psf file. Michel Espinoza-Fonseca (Wed Apr 06 2005 - 12:34:44 CDT)
- Nanotube psf file. mustapha.hamdi_at_ensi-bourges.fr (Wed Apr 06 2005 - 13:06:59 CDT)
- Duplicate lines in the output file ! Parag Adhangale (Wed Apr 06 2005 - 11:52:56 CDT)
- add water on the top of the protein border Xiaoqing Wang (Wed Apr 06 2005 - 09:11:47 CDT)
- FEP output in NAMD Vani Krishna (Tue Apr 05 2005 - 11:26:39 CDT)
- namd and node freeze Brady Chang (Tue Apr 05 2005 - 03:39:26 CDT)
- RATTLE and DNA Nicholas M Glykos (Tue Apr 05 2005 - 05:33:48 CDT)
- RE: problem running namd Michel Espinoza-Fonseca (Mon Apr 04 2005 - 13:48:02 CDT)
- problem running namd Michel Espinoza-Fonseca (Mon Apr 04 2005 - 11:54:45 CDT)
- problem running namd Michel Espinoza-Fonseca (Mon Apr 04 2005 - 11:18:01 CDT)
- Errors compiling NAMD 2.5 Koo Kee Kiat (Mon Apr 04 2005 - 01:46:34 CDT)
- binary restraint reference coordinates? Cameron Mura (Thu Mar 31 2005 - 20:31:42 CST)
- Charm++ problem on EM64T/Myrinet cluster Chona S. Guiang (Thu Mar 31 2005 - 16:08:38 CST)
- NAMD recognizes only one MPI process Randy Crawford (Thu Mar 31 2005 - 11:46:45 CST)
- conformational alignment Wen Li (Wed Mar 30 2005 - 15:21:26 CST)
- RE: glucose CHARMM force field Michel Espinoza-Fonseca (Tue Mar 29 2005 - 22:13:35 CST)
- glucose CHARMM force field Hyonseok Hwang (Tue Mar 29 2005 - 21:37:34 CST)
- multiple MD simulations Aaron Oakley (Mon Mar 28 2005 - 18:29:39 CST)
- socket closed error brady chang (Fri Mar 25 2005 - 14:54:01 CST)
- Modeling a polymer Glenn Johnson (Thu Mar 24 2005 - 13:44:29 CST)
- question about patch jz7_at_duke.edu (Thu Mar 24 2005 - 09:33:04 CST)
- pairlist distance debashis.sikdar_at_ndsu.edu (Wed Mar 23 2005 - 09:32:48 CST)
- pairlist distance debashis.sikdar_at_ndsu.edu (Tue Mar 22 2005 - 14:28:20 CST)
- path problems Michael Grabe (Tue Mar 22 2005 - 01:29:25 CST)
- Re: path problems Gengbin Zheng (Tue Mar 22 2005 - 01:37:52 CST)
- visualizing dynamics output Samuel Flores (Tue Mar 22 2005 - 11:31:31 CST)
- Re: visualizing dynamics output Brian Bennion (Tue Mar 22 2005 - 12:55:00 CST)
- RE: visualizing dynamics output Samuel Flores (Tue Mar 22 2005 - 13:51:07 CST)
- RE: visualizing dynamics output Michel Espinoza-Fonseca (Tue Mar 22 2005 - 14:17:12 CST)
- molecules distorted Samuel Flores (Tue Mar 22 2005 - 15:35:03 CST)
- RE: molecules distorted Michel Espinoza-Fonseca (Tue Mar 22 2005 - 15:37:19 CST)
- How to read charmm binary trajectory file using home-made C/C++ code Wei Zhuang (Tue Mar 22 2005 - 14:39:15 CST)
- visualizing dynamics output Samuel Flores (Tue Mar 22 2005 - 11:31:31 CST)
- Re: path problems Gengbin Zheng (Tue Mar 22 2005 - 01:37:52 CST)
- RE: running VMD from a script? -- oops, never mind! Samuel Flores (Mon Mar 21 2005 - 19:49:50 CST)
- psfgen for DNA Nicholas M Glykos (Mon Mar 21 2005 - 10:20:49 CST)
- running VMD from a script? Samuel Flores (Sun Mar 20 2005 - 18:22:23 CST)
- RE: question about par_all27_prot_lipid.inp Michel Espinoza-Fonseca (Sun Mar 20 2005 - 15:22:19 CST)
- question about par_all27_prot_lipid.inp Samuel Flores (Sun Mar 20 2005 - 01:34:58 CST)
- convert namd structure/coordinate files to gromacs topology file Glenn Johnson (Fri Mar 18 2005 - 14:00:54 CST)
- NAMD on new P4 Gan, Yong \(UMC-Student\) (Fri Mar 18 2005 - 13:04:54 CST)
- strange behaviour when running apoa1 on 1 processor Mauricio Carrillo Tripp (Thu Mar 17 2005 - 13:36:47 CST)
- isotropic pressure tensor Gan, Yong \(UMC-Student\) (Wed Mar 16 2005 - 21:56:49 CST)
- Bio-Image summer school in Paris this year Marc Baaden (Wed Mar 16 2005 - 05:42:59 CST)
- membrane files Gan, Yong \(UMC-Student\) (Tue Mar 15 2005 - 20:54:41 CST)
- computing resource Wei Chen (Mon Mar 14 2005 - 23:08:48 CST)
- namd and fftw Michel Espinoza-Fonseca (Mon Mar 14 2005 - 18:11:43 CST)
- "Hands-On" Workshop on Computational Biophysics David Brandon (Fri Mar 11 2005 - 15:23:27 CST)
- peridic boundary condition debashis.sikdar_at_ndsu.edu (Fri Mar 11 2005 - 09:08:37 CST)
- Re: peridic boundary condition Marc Q. Ma (Fri Mar 11 2005 - 10:38:15 CST)
- Re: peridic boundary condition Edward Patrick Obrien (Fri Mar 11 2005 - 13:09:43 CST)
- Re: peridic boundary condition Marc Q. Ma (Fri Mar 11 2005 - 13:15:31 CST)
- Re: peridic boundary condition Himanshu Khandelia (Fri Mar 11 2005 - 13:57:23 CST)
- Re: peridic boundary condition John Kerrigan (Fri Mar 11 2005 - 15:18:48 CST)
- Submitting jobs on myrinet...problem Edward Patrick Obrien (Fri Mar 11 2005 - 18:29:19 CST)
- Re: Submitting jobs on myrinet...problem Jerry Ebalunode (Fri Mar 11 2005 - 22:21:55 CST)
- Re: peridic boundary condition Jérôme Hénin (Fri Mar 11 2005 - 15:31:47 CST)
- Re: peridic boundary condition Marc Q. Ma (Fri Mar 11 2005 - 14:00:37 CST)
- Re: peridic boundary condition Marc Q. Ma (Fri Mar 11 2005 - 10:38:15 CST)
- namd2 mpi error Mauricio Carrillo Tripp (Thu Mar 10 2005 - 14:58:37 CST)
- flexible cell for MD simulations Michel Espinoza-Fonseca (Thu Mar 10 2005 - 16:25:17 CST)
- Compiling on Linux-PPC970-Myrinet-MPI-xlC Jordi Camps (Thu Mar 10 2005 - 12:57:47 CST)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Brian Bennion (Thu Mar 10 2005 - 14:11:29 CST)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Gengbin Zheng (Thu Mar 10 2005 - 15:54:56 CST)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Brian Bennion (Thu Mar 10 2005 - 15:59:33 CST)
- RE: Compiling on Linux-PPC970-Myrinet-MPI-xlC Jordi Camps (Thu Mar 10 2005 - 18:08:02 CST)
- RE: Compiling on Linux-PPC970-Myrinet-MPI-xlC Brian Bennion (Thu Mar 10 2005 - 18:22:43 CST)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Wed Mar 16 2005 - 00:06:21 CST)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Gengbin Zheng (Wed Mar 16 2005 - 00:24:54 CST)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Wed Mar 16 2005 - 04:37:07 CST)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Gengbin Zheng (Thu Mar 10 2005 - 15:54:56 CST)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Brian Bennion (Thu Mar 10 2005 - 14:11:29 CST)
- example scripts Himanshu Khandelia (Thu Mar 10 2005 - 10:03:53 CST)
- compiling Namd on amd64 olivier Walker (Thu Mar 10 2005 - 04:08:08 CST)
- Re: compiling Namd on amd64 Brian Bennion (Thu Mar 10 2005 - 10:20:46 CST)
- CAN'T FIND BOND PARAMETERS FOR BOND (error) sabri bora erdemli (Thu Mar 10 2005 - 03:23:02 CST)
- modeling sucrose Glenn Johnson (Wed Mar 09 2005 - 17:19:12 CST)
- loodking or topology file for zinc finger Wang Tianhua (Tue Mar 08 2005 - 19:43:02 CST)
- Re: G5 cluster Gengbin Zheng (Tue Mar 08 2005 - 16:41:06 CST)
- G5 clusters Michael Grabe (Tue Mar 08 2005 - 11:17:42 CST)
- NAMD restarts binary files Shirley Hui (Tue Mar 08 2005 - 10:13:08 CST)
- Installing NAMD Michel Espinoza-Fonseca (Mon Mar 07 2005 - 18:18:43 CST)
- Potential energies in TCL interface Eric Cyr (Mon Mar 07 2005 - 15:36:09 CST)
- Re: question (fwd) Michael Grabe (Mon Mar 07 2005 - 15:30:48 CST)
- atom specification in smd/tclforces for amber topology/parameter based systems Jerry Ebalunode (Mon Mar 07 2005 - 14:50:20 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Mon Mar 07 2005 - 13:37:11 CST)
- Re: namd on Altix Gengbin Zheng (Mon Mar 07 2005 - 13:39:49 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Mon Mar 07 2005 - 14:16:16 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Mon Mar 07 2005 - 15:00:02 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Mon Mar 07 2005 - 18:43:25 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Mon Mar 07 2005 - 19:06:35 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Tue Mar 08 2005 - 15:03:49 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Tue Mar 08 2005 - 16:57:08 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Tue Mar 08 2005 - 17:05:52 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Tue Mar 08 2005 - 17:17:46 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Tue Mar 08 2005 - 17:31:15 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Wed Mar 09 2005 - 13:33:35 CST)
- namd on Altix Michel Espinoza-Fonseca (Mon Mar 07 2005 - 13:14:07 CST)
- Influence of PME grid size and cell basis vectors over simulation result debashis.sikdar_at_ndsu.edu (Mon Mar 07 2005 - 13:01:19 CST)
- Patch Gan, Yong \(UMC-Student\) (Thu Mar 03 2005 - 17:28:35 CST)
- installing NAMD on opteron cluster with MPI Lina M Nilsson (Thu Mar 03 2005 - 16:06:13 CST)
- Re: clustermatic nodelist file Gengbin Zheng (Wed Mar 02 2005 - 21:29:40 CST)
- Problems with the nodelist file ! Parag Adhangale (Wed Mar 02 2005 - 16:38:13 CST)
- Not getting good speed up Mauricio Carrillo Tripp (Wed Mar 02 2005 - 16:37:18 CST)
- Re: Not getting good speed up Gengbin Zheng (Wed Mar 02 2005 - 21:42:39 CST)
- Re: Not getting good speed up Mauricio Carrillo Tripp (Thu Mar 03 2005 - 13:16:24 CST)
- Re: Not getting good speed up Gengbin Zheng (Thu Mar 03 2005 - 13:34:56 CST)
- Re: Not getting good speed up Mauricio Carrillo Tripp (Thu Mar 03 2005 - 13:44:55 CST)
- Re: Not getting good speed up Mauricio Carrillo Tripp (Fri Mar 11 2005 - 15:32:38 CST)
- Re: Not getting good speed up Gengbin Zheng (Fri Mar 11 2005 - 16:04:53 CST)
- Re: Not getting good speed up Mauricio Carrillo Tripp (Sat Mar 12 2005 - 15:38:06 CST)
- Re: Not getting good speed up Mauricio Carrillo Tripp (Tue Mar 15 2005 - 10:55:16 CST)
- Trouble with NAMD on Myrinet Edward Patrick Obrien (Tue Mar 15 2005 - 14:02:40 CST)
- Re: Trouble with NAMD on Myrinet Gengbin Zheng (Tue Mar 15 2005 - 14:14:14 CST)
- Re: Trouble with NAMD on Myrinet Edward Patrick Obrien (Wed Mar 16 2005 - 10:04:20 CST)
- Re: Re: Trouble with NAMD on Myrinet Gengbin Zheng (Wed Mar 16 2005 - 11:27:19 CST)
- Re: Not getting good speed up Dow_Hurst (Tue Mar 15 2005 - 12:31:11 CST)
- Re: Not getting good speed up Mauricio Carrillo Tripp (Thu Mar 03 2005 - 13:16:24 CST)
- Re: Not getting good speed up Gengbin Zheng (Wed Mar 02 2005 - 21:42:39 CST)
- difference between two kinds of dimers olivier Walker (Wed Mar 02 2005 - 06:19:56 CST)
- NAMD attempting to read FFTW Shirley Hui (Tue Mar 01 2005 - 13:59:21 CST)
- NAMD_utilities Wei Chen (Tue Mar 01 2005 - 12:43:56 CST)
- capping using Amber FF Hui-Hsu Tsai (Tue Mar 01 2005 - 12:32:24 CST)
- Hexagonal cell and PME grid. Nicholas M Glykos (Tue Mar 01 2005 - 05:17:44 CST)
- Kinetic energy Gan, Yong \(UMC-Student\) (Fri Feb 25 2005 - 12:55:09 CST)
- Amber and SHAKE algorimth Marcela P.Aliste (Thu Feb 24 2005 - 16:14:26 CST)
- PMEGridSize Glenn Johnson (Thu Feb 24 2005 - 15:25:03 CST)
- NMAD job abnormally killed with PBS Nicolas Sapay (Thu Feb 24 2005 - 12:09:19 CST)
- warning on unique coordinates Stern, Julie (Wed Feb 23 2005 - 15:07:19 CST)
- cellOrigin Marc Q. Ma (Tue Feb 22 2005 - 14:06:04 CST)
- Pressure tensor and periodic boundary condition Gan, Yong \(UMC-Student\) (Mon Feb 21 2005 - 21:40:58 CST)
- writeback periodic cell info in dcd output Marc Q. Ma (Mon Feb 21 2005 - 16:16:01 CST)
- Lipid membrane simulation by NAMD Gan, Yong \(UMC-Student\) (Fri Feb 18 2005 - 17:40:25 CST)
- energy Swarna Patra (Thu Feb 17 2005 - 16:58:36 CST)
- alchemify FEP Wei Chen (Thu Feb 17 2005 - 13:14:20 CST)
- constraining center of mass-constrained MD Vani Krishna (Thu Feb 17 2005 - 02:51:12 CST)
- rotation constraint angular velocity Xiongce Zhao (Wed Feb 16 2005 - 10:32:14 CST)
- RE: using namd to compute energies Wolbach, Jeffrey P \(WOLBACH\) (Wed Feb 16 2005 - 07:30:41 CST)
- 1 D Periodic Boundary Xiongce Zhao (Tue Feb 15 2005 - 14:43:42 CST)
- using namd to compute energies Leandro Martinez (Tue Feb 15 2005 - 13:24:20 CST)
- how to image molecules back into a PBC box Xiongce Zhao (Tue Feb 15 2005 - 09:08:21 CST)
- RE: conditional statements in conf files Glenn Johnson (Mon Feb 14 2005 - 15:49:46 CST)
- conditional statements in conf files Glenn Johnson (Mon Feb 14 2005 - 14:59:02 CST)
- question on tcl script for rmsd calculation Olya Kravchenko (Mon Feb 14 2005 - 13:44:41 CST)
- Complementary programs for NAMD Glenn Johnson (Mon Feb 14 2005 - 13:32:24 CST)
- Analysis of NAMD output with CHARMM Leyla Celik (Mon Feb 14 2005 - 02:47:42 CST)
- Unprotonating GLU, ASP Gaurav Sharma (Sun Feb 13 2005 - 18:14:31 CST)
- psfgen error "Missing atom for conformation definition" bora erdemli (Sat Feb 12 2005 - 06:16:30 CST)
- RE: namdplot not working Glenn Johnson (Fri Feb 11 2005 - 17:30:33 CST)
- Re: namdplot not working vivek sharma (Fri Feb 11 2005 - 16:04:06 CST)
- namdplot not working Glenn Johnson (Fri Feb 11 2005 - 14:39:45 CST)
- namd2.5 on linux-cluster Alexe Bojovschi (Wed Feb 09 2005 - 04:41:43 CST)
- XPLOR topology to CHARMM bora erdemli (Wed Feb 09 2005 - 03:01:15 CST)
- Protein moving out of PBC water box Leyla Celik (Tue Feb 08 2005 - 15:23:31 CST)
- Question about Constraint failure in RATTLE algorithm for atom Hrant Gharabekyan (Tue Feb 08 2005 - 05:06:46 CST)
- PMF Calculation matteo (Tue Feb 08 2005 - 04:38:20 CST)
- NAMD crashes with LES option ON Karunesh Arora (Mon Feb 07 2005 - 14:07:18 CST)
- Re: question on running NAMD2 using Amber files Wen Li (Mon Feb 07 2005 - 12:15:41 CST)
- question on running NAMD2 using Amber files (fwd) Wen Li (Mon Feb 07 2005 - 10:25:32 CST)
- Complie NAMD on Suse Linux Jason Lee (Mon Feb 07 2005 - 09:32:02 CST)
- question on running NAMD2 using Amber files Wen Li (Mon Feb 07 2005 - 08:40:56 CST)
- gradient nan Hemant Kushwaha (Mon Feb 07 2005 - 00:17:04 CST)
- SMD by pulling two groups apart Ekta Khurana (Fri Feb 04 2005 - 16:27:06 CST)
- area of a hydrophobic patch Narender Singh Maan (Wed Feb 02 2005 - 23:23:24 CST)
- Complie NAMD on Suse Linux cunning cunning (Thu Feb 03 2005 - 08:18:46 CST)
- parameters for NAD,NAG,NAP bora erdemli (Thu Feb 03 2005 - 03:39:00 CST)
- FEP Wei Chen (Tue Feb 01 2005 - 11:15:24 CST)
- force constraints Swarna Patra (Mon Jan 31 2005 - 19:49:07 CST)
- Hi, call NAMD from C Jerry Xu (Mon Jan 31 2005 - 09:28:44 CST)
- simulated annealing step size Peter Bazeley (Fri Jan 28 2005 - 20:23:19 CST)
- electrostatics under spherical harmonic conditions Giovanni Bellesia (Fri Jan 28 2005 - 13:59:57 CST)
- tRNA simulation psf file generation explicit solvent and ions Tom Caulfield (Thu Jan 27 2005 - 02:29:47 CST)
- Qestions about NPT simulations. Lv Shouqin (Wed Jan 26 2005 - 07:29:47 CST)
- Catdcd Naveen Michaud-Agrawal (Wed Jan 26 2005 - 08:44:45 CST)
- BUG ALERT: Mother atom with hydrogenGroupSize of 0! Xiaoqing Wang (Mon Jan 24 2005 - 01:26:21 CST)
- NAMD on IBM cluster AIX-RS6000 Harindar Keer (Fri Jan 21 2005 - 18:46:29 CST)
- Question about pair interaction feature Eric Peterson (Thu Jan 20 2005 - 17:43:49 CST)
- resetting restartfreq parameter Peter Bazeley (Thu Jan 20 2005 - 17:17:16 CST)
- Rotating a structure about an atom Pijush Ghosh (Wed Jan 19 2005 - 12:47:56 CST)
- DOWSER Charles Danko (Tue Jan 18 2005 - 16:20:06 CST)
- hydrogens collapsing lc_at_chem.au.dk (Tue Jan 18 2005 - 08:46:23 CST)
- Obtain message from MD Xiaoqing Wang (Tue Jan 18 2005 - 01:30:23 CST)
- smd and loadforces Leandro Martinez (Mon Jan 17 2005 - 11:06:50 CST)
- about rigid bonds mashaojie163 (Mon Jan 17 2005 - 07:24:39 CST)
- Compiling the NAMD on HPUX-ia64 system Error! κ¿ (Sat Jan 15 2005 - 08:35:00 CST)
- charm++ compile problem on x86_64 Steven A. DuChene (Fri Jan 14 2005 - 15:24:02 CST)
- scyld no longer a supported option for building charm++ ? Steven A. DuChene (Fri Jan 14 2005 - 14:30:10 CST)
- last call for early registrations for "Horizons2005" Vlad Cojocaru (Fri Jan 14 2005 - 07:19:00 CST)
- How to Compile NAMD on HPUX-ia64 system~ κ¿ (Fri Jan 14 2005 - 04:56:14 CST)
- extracting time from DCDs nordgren_at_sas.upenn.edu (Thu Jan 13 2005 - 19:54:30 CST)
- rattle errors. Brian Bennion (Thu Jan 13 2005 - 10:56:25 CST)
- segmentation violation!! bora erdemli (Thu Jan 13 2005 - 02:15:19 CST)
- Re: segmentation violation!! Brian Bennion (Thu Jan 13 2005 - 10:48:11 CST)
- Re: segmentation violation!! bora erdemli (Fri Jan 14 2005 - 03:06:55 CST)
- Re: segmentation violation!! Brian Bennion (Fri Jan 14 2005 - 10:20:49 CST)
- Re: segmentation violation!! bora erdemli (Sun Jan 16 2005 - 03:59:08 CST)
- Re: segmentation violation!! Brian Bennion (Tue Jan 18 2005 - 10:34:47 CST)
- Re: segmentation violation!! Robert Brunner (Tue Jan 18 2005 - 11:05:00 CST)
- Re: segmentation violation!! bora erdemli (Fri Jan 14 2005 - 03:06:55 CST)
- Re: segmentation violation!! Brian Bennion (Thu Jan 13 2005 - 10:48:11 CST)
- success with opteron myrinet mpi etc Damon Smith (Thu Jan 13 2005 - 01:28:30 CST)
- Electric Field Swarna Patra (Wed Jan 12 2005 - 16:57:02 CST)
- multiple jobs on a cluster Cheri M Turman (Wed Jan 12 2005 - 15:55:42 CST)
- constraint failure Xiaoqing Wang (Tue Jan 11 2005 - 21:07:08 CST)
- equilibrated the system Xiaoqing Wang (Tue Jan 11 2005 - 08:43:17 CST)
- AMD64 or PIV Prescott ... Slawomir Orlowski (Tue Jan 11 2005 - 05:52:48 CST)
- namdstats lc_at_chem.au.dk (Tue Jan 11 2005 - 01:54:54 CST)
- thermodynamic integration and NAMD: soft-core or "separation-shifted" vdw potentials Philip Fowler (Mon Jan 10 2005 - 11:12:41 CST)
- Error in when using charmrun Eric Peterson (Sat Jan 08 2005 - 20:39:45 CST)
- Harmonic restraints for moving residue positions?? Charles Danko (Sat Jan 08 2005 - 15:03:50 CST)
- restarting a simulation accurately Stern, Julie (Sat Jan 08 2005 - 14:32:41 CST)
- tclForces - addforce to group of atoms Jan Saam (Fri Jan 07 2005 - 17:27:40 CST)
- tclForces - addforce to group of atoms Jan Saam (Fri Jan 07 2005 - 17:01:13 CST)
- namd on lemieux Stern, Julie (Fri Jan 07 2005 - 11:51:53 CST)
- parameters for NVT ensemble lc_at_chem.au.dk (Fri Jan 07 2005 - 04:51:07 CST)
- Compiling Damon Smith (Thu Jan 06 2005 - 19:02:04 CST)
- tcoupling coefficient Peter Bazeley (Wed Jan 05 2005 - 06:31:07 CST)
- Re: Bug alert!!! bora erdemli (Tue Jan 04 2005 - 01:13:37 CST)
- increase in energy over time Peter Bazeley (Mon Jan 03 2005 - 17:27:45 CST)
- prmtop reading error Stern, Julie (Sun Jan 02 2005 - 15:35:42 CST)
- About charm++/namd on AMD64 cluster q=F5=D0=A1=C7=E5?= (Sun Jan 02 2005 - 02:01:32 CST)
- Re: clustermatic 4 and 5 Namd/charm Rene Salmon (Sat Jan 01 2005 - 14:56:56 CST)
Last message date: Fri Dec 29 2006 - 23:10:16 CST
Archived on: Wed Feb 29 2012 - 15:42:59 CST
3455 messages sorted by:
[ author ]
[ date ]
[ subject ]
[ attachment ]
About this archive
