NAMD-L: By Thread
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About this archive
Starting: Mon Sep 08 2003 - 09:54:14 CDT
Ending: Sat Nov 07 2009 - 16:54:28 CST
- Error in Minimization Ale Gomez (Sat Nov 07 2009 - 10:45:24 CST)
- Is it a bug? TCL Script may Lead to Overflow Fred (Rui FENG) (Sat Nov 07 2009 - 03:09:28 CST)
- Tuning NAMD CUDA? Ronald Salesky (Fri Nov 06 2009 - 18:07:14 CST)
- strange error from NAMD with CUDA t s (Thu Nov 05 2009 - 13:55:14 CST)
- NAMD-problem jose correa (Thu Nov 05 2009 - 17:29:30 CST)
- Atom constraint in certain direction Priyan Amaras (Thu Nov 05 2009 - 11:15:31 CST)
- molecular dynamics simulation ipsita basu (Thu Nov 05 2009 - 04:35:33 CST)
- Running NAMD w/ CUDA under Linux Ronald Salesky (Wed Nov 04 2009 - 21:23:30 CST)
- Read dcd file and calculate (distance/constraint energy Vs snapshots) using NAMD priyodorshi satpati (Wed Nov 04 2009 - 11:05:33 CST)
- Re: ibverbs crash Bjoern Olausson (Wed Nov 04 2009 - 08:38:45 CST)
- TIP4P Luca Mammucari (Tue Nov 03 2009 - 17:07:10 CST)
- TIP4P topology Luca Bellucci (Tue Nov 03 2009 - 14:24:04 CST)
- ibverbs crash David A. Horita (Tue Nov 03 2009 - 14:17:17 CST)
- (no subject) l.mammucari_at_tin.it (Mon Nov 02 2009 - 15:47:14 CST)
- (no subject) Luca M. (Mon Nov 02 2009 - 14:33:36 CST)
- Abnormal EOF found -buffer=*END* Patrick Yee (Mon Nov 02 2009 - 12:35:52 CST)
- PMEGridSpacing DimitryASuplatov (Sat Oct 31 2009 - 05:46:04 CDT)
- How to apply an unsteady magnetic field? fereshteh moradi (Sun Oct 25 2009 - 01:52:29 CDT)
- Namd benchmark problem Sangamesh B (Thu Oct 22 2009 - 10:29:17 CDT)
- Namd benchmark problem Sangamesh B (Sat Oct 24 2009 - 02:12:05 CDT)
- Re: Namd benchmark problem Axel Kohlmeyer (Sat Oct 24 2009 - 11:30:45 CDT)
- Re: Namd benchmark problem Sangamesh B (Sun Oct 25 2009 - 01:46:29 CDT)
- Re: Namd benchmark problem Joshua Adelman (Sun Oct 25 2009 - 08:18:23 CDT)
- Re: Namd benchmark problem Axel Kohlmeyer (Sun Oct 25 2009 - 15:48:23 CDT)
- Re: Namd benchmark problem Bernardo Sosa Padilla Araujo (Mon Oct 26 2009 - 00:10:25 CDT)
- Re: Namd benchmark problem Nicholas M Glykos (Mon Oct 26 2009 - 04:57:22 CDT)
- Re: Namd benchmark problem Axel Kohlmeyer (Mon Oct 26 2009 - 08:26:03 CDT)
- Re: Namd benchmark problem Nicholas M Glykos (Mon Oct 26 2009 - 09:14:36 CDT)
- Re: Namd benchmark problem Axel Kohlmeyer (Mon Oct 26 2009 - 09:45:46 CDT)
- Re: Namd benchmark problem Nicholas M Glykos (Mon Oct 26 2009 - 10:08:01 CDT)
- Re: Namd benchmark problem Axel Kohlmeyer (Mon Oct 26 2009 - 08:16:55 CDT)
- Re: Namd benchmark problem Axel Kohlmeyer (Sat Oct 24 2009 - 11:30:45 CDT)
- Namd benchmark problem Sangamesh B (Sat Oct 24 2009 - 02:12:05 CDT)
- Molecular dynamics of multiple organic molecules with NAMD B (Thu Oct 22 2009 - 09:39:06 CDT)
- Error on renaming file: Permission denied Stephen Hicks (Mon Jun 04 2007 - 00:38:28 CDT)
- Hydrogen molecule model Mikhail Suyetin (Fri Oct 30 2009 - 10:42:19 CDT)
- issues with AutoPSF for a cyclodextrin CHINDEA Vlad (Thu Oct 29 2009 - 18:32:50 CDT)
- RAMD in NAMD; bugs and new version 4.0 Vlad Cojocaru (Thu Oct 29 2009 - 11:13:39 CDT)
- About APBS calculation «J ¦¼¯Â (Thu Oct 29 2009 - 09:22:48 CDT)
- Using restraints DimitryASuplatov (Wed Oct 28 2009 - 10:55:44 CDT)
- Re: NAMD2.7 scaling problems DimitryASuplatov (Wed Oct 28 2009 - 08:30:44 CDT)
- NAMD2.7 scaling problems DimitryASuplatov (Wed Oct 28 2009 - 04:06:13 CDT)
- abnormal water surface after nvt and npt for POPC membrane pxq ÅÓÑ©ÇÛ (Tue Oct 27 2009 - 19:57:58 CDT)
- order parameter, lipid segments as vectors Raul Araya (Tue Oct 27 2009 - 08:48:32 CDT)
- Tcl forces Myunggi Yi (Mon Oct 26 2009 - 13:12:50 CDT)
- Modeling familial amyloidotic polyneuropathy drmartin_at_fizyka.umk.pl (Mon Oct 26 2009 - 07:04:03 CDT)
- Random Expulsion MD (REMD) kristian krantz (Mon Oct 26 2009 - 06:07:11 CDT)
- namd cvs memory leak? BIN ZHANG (Thu Oct 22 2009 - 18:12:08 CDT)
- Pair interaction runtime analysis skipping dcd frames lucie delemotte (Thu Oct 22 2009 - 09:30:08 CDT)
- fresh file not ready to read? BIN ZHANG (Thu Oct 22 2009 - 01:46:10 CDT)
- Modification of equlibrated simulation box namd_chcwaaa_at_yahoo.com.cn (Wed Oct 21 2009 - 00:36:37 CDT)
- Re: CG bead definition BIN ZHANG (Tue Oct 20 2009 - 15:12:04 CDT)
- unsubscribe Vinit Rege (Tue Oct 20 2009 - 13:26:56 CDT)
- Fwd: vmd-l: CG bead definition BIN ZHANG (Tue Oct 20 2009 - 11:19:30 CDT)
- COARSE GRAINED WATER MODEL Valeria Marquez (Tue Oct 20 2009 - 08:52:10 CDT)
- smd output (v2.6) David A. Horita (Mon Oct 19 2009 - 12:04:05 CDT)
- Water Sphere Solvation Peter Murphy (Sun Oct 18 2009 - 08:41:38 CDT)
- Tolerance for SHAKE Nicholas M Glykos (Sun Oct 18 2009 - 07:58:20 CDT)
- zeroMomentum command A D (Fri Oct 16 2009 - 18:29:08 CDT)
- tcl force Seungho Choe (Fri Oct 16 2009 - 16:34:58 CDT)
- Tcl forces Myunggi Yi (Fri Oct 16 2009 - 15:06:45 CDT)
- ATP and Stream files Luis Agullo (LAB) (Fri Oct 16 2009 - 03:39:30 CDT)
- Slow heating in namd Pavan G (Thu Oct 15 2009 - 09:10:02 CDT)
- Ionization with VMD Luis Agullo (LAB) (Thu Oct 15 2009 - 09:07:13 CDT)
- ATP and Stream files Luis Agullo (LAB) (Thu Oct 15 2009 - 07:49:58 CDT)
- spontaneous system explosion after 2 ns of normal run Roman Petrenko (Wed Oct 14 2009 - 22:57:34 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Roman Petrenko (Wed Oct 14 2009 - 23:09:36 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Luis Agullo (LAB) (Thu Oct 15 2009 - 08:40:06 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Axel Kohlmeyer (Thu Oct 15 2009 - 10:01:00 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Roman Petrenko (Thu Oct 15 2009 - 10:22:44 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Axel Kohlmeyer (Thu Oct 15 2009 - 11:15:23 CDT)
- Re: spontaneous system explosion after 2 ns of normal run daniel aguayo (Thu Oct 15 2009 - 19:46:12 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Roman Petrenko (Sun Oct 18 2009 - 22:59:08 CDT)
- Fullerene topology Austin B. Yongye (Mon Oct 26 2009 - 13:40:17 CDT)
- Simulation crash due to charmrun error Rukman Hertadi (Tue Oct 27 2009 - 03:38:20 CDT)
- Re: Fullerene topology Luca Muccioli (Wed Oct 28 2009 - 10:55:11 CDT)
- Re: Fullerene topology Austin B. Yongye (Wed Oct 28 2009 - 11:41:49 CDT)
- Re: Fullerene topology Luca Muccioli (Wed Oct 28 2009 - 15:31:38 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Jian Liu (Mon Oct 19 2009 - 01:45:24 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Roman Petrenko (Thu Oct 15 2009 - 10:22:44 CDT)
- center of mass of dummyAtom in colvar BIN ZHANG (Wed Oct 14 2009 - 16:57:13 CDT)
- Unusual bond between residues: 0 (none) and 1 (protein) Song, Hyundeok (songhk) (Wed Oct 14 2009 - 11:33:15 CDT)
- How to fix relative position of a group Yang (Tue Oct 13 2009 - 15:40:53 CDT)
- Re: How to fix relative position of a group JC Gumbart (Tue Oct 13 2009 - 19:27:40 CDT)
- Re: PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG Sebastian Stolzenberg (Wed Nov 04 2009 - 18:10:32 CST)
- Re: Re: PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG Sebastian Stolzenberg (Sat Nov 07 2009 - 12:33:32 CST)
- temperature calculations from velocities in NAMD? Sebastian Stolzenberg (Sat Nov 07 2009 - 13:32:41 CST)
- Re: temperature calculations from velocities in NAMD? Axel Kohlmeyer (Sat Nov 07 2009 - 14:21:40 CST)
- Re: temperature calculations from velocities in NAMD? Sebastian Stolzenberg (Sat Nov 07 2009 - 16:31:48 CST)
- Re: temperature calculations from velocities in NAMD? Axel Kohlmeyer (Sat Nov 07 2009 - 16:55:13 CST)
- Re: PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG Sebastian Stolzenberg (Wed Nov 04 2009 - 18:10:32 CST)
- Re: How to fix relative position of a group JC Gumbart (Tue Oct 13 2009 - 19:27:40 CDT)
- size of integration step Jorgen Simonsen (Tue Oct 13 2009 - 10:44:47 CDT)
- Incorrect Atom Count in binary file Yogesh Aher (Tue Oct 13 2009 - 03:42:44 CDT)
- Generation of average trajectory mon_sharma_at_research.iiit.ac.in (Mon Oct 12 2009 - 02:26:02 CDT)
- restraining the COM of a group of atoms BIN ZHANG (Fri Oct 09 2009 - 19:19:56 CDT)
- Lennard-Jones potential in CHARMM Lixia Jin Day (Thu Oct 08 2009 - 16:19:16 CDT)
- nonbonded potential BIN ZHANG (Thu Oct 08 2009 - 00:19:30 CDT)
- about restart namd_chcwaaa_at_yahoo.com.cn (Thu Oct 08 2009 - 06:46:07 CDT)
- NAMD CUDA release steve.kaminski_at_mail.tu-berlin.de (Wed Oct 07 2009 - 16:01:12 CDT)
- followup question on error calculation in ABF Giovanni Bellesia (Wed Oct 07 2009 - 13:50:55 CDT)
- Tcl force Chaloin Laurent (Wed Oct 07 2009 - 05:22:01 CDT)
- How to put a COM restraint on a membrane protein? A D (Tue Oct 06 2009 - 18:03:25 CDT)
- constraint energy contributions Michael Thomas (Tue Oct 06 2009 - 06:33:25 CDT)
- PCA Calculation Anirban Ghosh (Tue Oct 06 2009 - 00:13:08 CDT)
- R.E.D.-III.3 tools release - q4md-forcefieldtools.org FyD (Sun Oct 04 2009 - 09:37:06 CDT)
- running namd in parallel Jorgen Simonsen (Sat Oct 03 2009 - 16:18:57 CDT)
- CMAP w/ D-amino acid Ziemys, Arturas (Fri Oct 02 2009 - 10:51:24 CDT)
- Changing the atomtype of a particle on the fly BIN ZHANG (Fri Oct 02 2009 - 01:15:07 CDT)
- error termination Sridhar Vaddadi (Fri Oct 02 2009 - 11:08:02 CDT)
- Minimisation Protocol Philip Peartree (Fri Oct 02 2009 - 11:36:49 CDT)
- Re: Changing the atomtype of a particle on the fly Axel Kohlmeyer (Fri Oct 02 2009 - 13:09:12 CDT)
- Re: Changing the atomtype of a particle on the fly Axel Kohlmeyer (Fri Oct 02 2009 - 13:30:57 CDT)
- Re: Changing the atomtype of a particle on the fly BIN ZHANG (Fri Oct 02 2009 - 13:50:21 CDT)
- Re: Changing the atomtype of a particle on the fly Axel Kohlmeyer (Fri Oct 02 2009 - 14:57:43 CDT)
- Re: Changing the atomtype of a particle on the fly daniel aguayo (Sun Oct 04 2009 - 18:59:00 CDT)
- Re: Changing the atomtype of a particle on the fly Axel Kohlmeyer (Mon Oct 05 2009 - 02:14:41 CDT)
- NAMD 2.7b1 on Lonestar Jufang Shan (Mon Oct 05 2009 - 10:44:23 CDT)
- Re: Changing the atomtype of a particle on the fly Axel Kohlmeyer (Fri Oct 02 2009 - 13:30:57 CDT)
- questions regarding new single node box for NAMD: re components, CUDA, Fermi Biff Forbush (Thu Oct 01 2009 - 17:27:06 CDT)
- Loop Andres Morales N (Thu Oct 01 2009 - 07:59:27 CDT)
- heating a system Bernardo Sosa Padilla Araujo (Thu Oct 01 2009 - 11:51:10 CDT)
- ABF + LES Ziemys, Arturas (Thu Oct 01 2009 - 11:45:38 CDT)
- namd2.7b1, tip4p, and dummies Edward Lyman (Wed Sep 30 2009 - 13:56:47 CDT)
- Re: vmd-l: namd2.7b1, tip4p, and dummies Joshua D. Moore (Wed Sep 30 2009 - 05:24:34 CDT)
- NAMD 2.7b1 ABF + free energy windows Reichert, David (Tue Sep 29 2009 - 15:33:48 CDT)
- g(r) GUI Plugin problem Branko (Tue Sep 29 2009 - 05:32:03 CDT)
- a timing question; 206,000atoms > 512cores not good Thomas C. Bishop (Mon Sep 28 2009 - 12:17:07 CDT)
- Why is the temperature set different in the membrane proteins tutorial? FengXian Zheng (Sat Sep 26 2009 - 19:58:28 CDT)
- NAMD2.7b1 performance Myunggi Yi (Fri Sep 25 2009 - 08:54:33 CDT)
- Namd not detecting my CUDA enabled GPU nicolabrisotto (Thu Sep 24 2009 - 11:07:35 CDT)
- where can I find the file: cornell.rtf (in bionano tutorial) Jian Liu (Thu Sep 24 2009 - 02:03:38 CDT)
- How the seed influences the molecular dynamics simulations? Agostino (Wed Sep 23 2009 - 04:15:26 CDT)
- extracting info from output files Rajiv Abhyankar (Tue Sep 22 2009 - 13:26:08 CDT)
- Re: extracting info from output files Axel Kohlmeyer (Tue Sep 22 2009 - 14:03:12 CDT)
- Re: extracting info from output files Giacomo Fiorin (Tue Sep 22 2009 - 15:12:05 CDT)
- Re: extracting info from output files Rajiv Abhyankar (Tue Sep 22 2009 - 17:56:19 CDT)
- RE: extracting info from output files Zumot, Elia Nabil (Tue Sep 22 2009 - 16:22:40 CDT)
- Precision of Coordinate data Rick Calloway (Tue Sep 22 2009 - 12:08:34 CDT)
- Re: Precision of Coordinate data Axel Kohlmeyer (Tue Sep 22 2009 - 13:22:47 CDT)
- help requested Sridhar Vaddadi (Wed Sep 23 2009 - 11:23:36 CDT)
- topology files Sridhar Vaddadi (Wed Sep 23 2009 - 13:59:02 CDT)
- Re: topology files Ramya Gamini (Wed Sep 23 2009 - 17:17:28 CDT)
- RE: topology files Sridhar Vaddadi (Wed Sep 23 2009 - 17:37:20 CDT)
- RE: topology files Sridhar Vaddadi (Thu Sep 24 2009 - 13:17:26 CDT)
- Re: topology files Axel Kohlmeyer (Thu Sep 24 2009 - 14:16:17 CDT)
- psfgen Sridhar Vaddadi (Wed Sep 23 2009 - 17:11:37 CDT)
- RE: pdb file Sridhar Vaddadi (Thu Sep 24 2009 - 11:34:38 CDT)
- topology files Sridhar Vaddadi (Wed Sep 23 2009 - 13:59:02 CDT)
- Do top_all27_prot_na.inp and cornell.prm share the same naming rules of atom types? ºÎع»Ô (Tue Sep 22 2009 - 02:51:56 CDT)
- GPU Selection in NAMD CUDA Ron Stubbs (Mon Sep 21 2009 - 14:56:42 CDT)
- adding specific forces between atoms Michael Zimmermann (Mon Sep 21 2009 - 15:44:48 CDT)
- Kemp elimination substrate charmm parameters Bernardo Sosa Padilla Araujo (Mon Sep 21 2009 - 15:41:01 CDT)
- Regarding Lipid Order Parameter Calculation Jagan Mohan (Mon Sep 21 2009 - 00:54:18 CDT)
- ABF calculation - normalization of the PMF Giovanni Bellesia (Sat Sep 19 2009 - 16:59:46 CDT)
- Replay to Parametrizing a novel residue] Branko (Fri Sep 18 2009 - 13:58:11 CDT)
- Parametrizing a novel residue Q=C1=D2=D8=D1_=FB=C1=CC=C1=C5=D7=C1?= (Fri Sep 18 2009 - 10:25:18 CDT)
- About NAN error cong chen (Fri Sep 18 2009 - 01:35:51 CDT)
- How to access velocity coordinates from within TclForces script Patrick Hogan (Thu Sep 17 2009 - 14:43:21 CDT)
- how to get psf files of DNA but not RNA with psfgen? ºÎع»Ô (Thu Sep 17 2009 - 06:25:02 CDT)
- can't load forces in tclforces James Servantie (Thu Sep 17 2009 - 05:54:21 CDT)
- AlF4 Laurent Chaloin (Thu Sep 17 2009 - 04:54:14 CDT)
- scripts for starting namd with condor John Wise (Wed Sep 16 2009 - 17:06:26 CDT)
- FAD topology and parameters of FAD jose correa (Wed Sep 16 2009 - 11:21:58 CDT)
- how to use volmap analysing a series of dcd. liupeng012_at_mail.nankai.edu.cn (Wed Sep 16 2009 - 08:39:50 CDT)
- Re: NVT with truncated octahedron or with sphere? Werner Crous (Wed Sep 16 2009 - 06:04:31 CDT)
- FATAL ERROR: Couldn't open DCD file ubq_wb_eq.dcd: No such file or directory Bernardo Sosa Padilla Araujo (Tue Sep 15 2009 - 18:26:25 CDT)
- NVT with truncated octahedron or with sphere? Werner Crous (Tue Sep 15 2009 - 03:03:06 CDT)
- Temperature rescaling vs. reassignment Luis Agullo (LAB) (Tue Sep 15 2009 - 09:26:48 CDT)
- Visit my Netlog profile Moumita Maiti (Tue Sep 15 2009 - 00:07:31 CDT)
- question about FEP soft-core yun luo (Mon Sep 14 2009 - 15:03:16 CDT)
- Re: CUDA-accelerated NAMD does not support NBFIX parameters [RESOLVED] Héctor Urbina (Mon Sep 14 2009 - 07:24:35 CDT)
- Regarding ABF Simulation Jagan Mohan (Mon Sep 14 2009 - 04:48:19 CDT)
- CUDA-accelerated NAMD does not support NBFIX parameters Héctor Urbina (Sun Sep 13 2009 - 13:47:33 CDT)
- Saving a subset of atoms Austin B. Yongye (Fri Sep 11 2009 - 12:32:44 CDT)
- Regarding NAMD CPU usage Amr Zeinalabideen Majul (Fri Sep 11 2009 - 08:22:08 CDT)
- atomic structure of some surfaces Roman Petrenko (Thu Sep 10 2009 - 19:57:14 CDT)
- FAD-parameters jose correa (Thu Sep 10 2009 - 13:50:33 CDT)
- [off topic] The mailing list's mailer ... Nicholas M Glykos (Wed Sep 09 2009 - 12:50:58 CDT)
- Implicit membrane models Austin B. Yongye (Wed Sep 09 2009 - 09:03:53 CDT)
- Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Tue Sep 08 2009 - 03:12:04 CDT)
- problems of "Stray PME grid charges" pxq ÅÓÑ©ÇÛ (Tue Sep 08 2009 - 09:40:44 CDT)
- Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Tue Sep 08 2009 - 03:13:02 CDT)
- (no subject) Jim Phillips (Tue Sep 08 2009 - 17:21:54 CDT)
- PMF: free energy calcs in "grow" phase? Sebastian Stolzenberg (Fri Sep 04 2009 - 15:57:00 CDT)
- CAN'T FIND DIHEDRAL PARAMETERS FOR CN8B CN7 ON5 HN5 Sujata Sovani (Fri Sep 04 2009 - 15:35:56 CDT)
- Re: vmd-l: rmsd matrix Cesar Millan (Thu Sep 03 2009 - 11:23:20 CDT)
- Membrane simulations Austin B. Yongye (Tue Sep 01 2009 - 10:24:36 CDT)
- CHARMM to NAMD Yang MIngjun (Tue Sep 01 2009 - 09:03:13 CDT)
- Re-posting - Methylated Histidine topology file Sujata Sovani (Mon Aug 31 2009 - 12:47:16 CDT)
- Methylated Histidine topology file Sujata Sovani (Mon Aug 31 2009 - 12:38:03 CDT)
- Periodic boundary conditions in membrane simulation jouko_at_uchicago.edu (Mon Aug 31 2009 - 11:56:22 CDT)
- Doubts and problem in ABF simulations Paulo Cesar Telles de Souza (Mon Aug 31 2009 - 11:00:57 CDT)
- PMF via constrained dynamics in NAMD satya work (Mon Aug 31 2009 - 09:01:43 CDT)
- for your suggestions on Pressure Control of transmembrane protein (GPCR) pxq ÅÓÑ©ÇÛ (Sun Aug 30 2009 - 22:18:47 CDT)
- Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. Mike Kuiper (Sun Aug 30 2009 - 03:54:57 CDT)
- Re: Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. Gianluca Interlandi (Sun Aug 30 2009 - 14:11:25 CDT)
- Re: Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. Roman Petrenko (Sun Aug 30 2009 - 16:06:26 CDT)
- Aslos End'tasa (Fri Aug 28 2009 - 11:55:17 CDT)
- hole on the surface of the waterbox Mert Gür (Fri Aug 28 2009 - 05:08:09 CDT)
- Re: hole on the surface of the waterbox Ana Vila Verde (Fri Aug 28 2009 - 05:54:06 CDT)
- Re: hole on the surface of the waterbox Mert Gür (Fri Aug 28 2009 - 06:12:25 CDT)
- Re: hole on the surface of the waterbox Ana Vila Verde (Fri Aug 28 2009 - 06:19:41 CDT)
- Re: hole on the surface of the waterbox Mert Gür (Fri Aug 28 2009 - 07:20:09 CDT)
- Re: hole on the surface of the waterbox Ana Vila Verde (Fri Aug 28 2009 - 07:26:14 CDT)
- Re: hole on the surface of the waterbox Mert Gür (Fri Aug 28 2009 - 07:36:16 CDT)
- Re: hole on the surface of the waterbox Ana Vila Verde (Fri Aug 28 2009 - 07:48:35 CDT)
- Re: hole on the surface of the waterbox Mert Gür (Fri Aug 28 2009 - 13:45:03 CDT)
- Re: hole on the surface of the waterbox Mert Gür (Fri Aug 28 2009 - 06:12:25 CDT)
- Re: hole on the surface of the waterbox Nicholas M Glykos (Fri Aug 28 2009 - 07:38:00 CDT)
- Re: hole on the surface of the waterbox Ana Vila Verde (Fri Aug 28 2009 - 05:54:06 CDT)
- ERROR: Constraint failure in RATTLE algorithm for atom 9080! gurunath katagi (Fri Aug 28 2009 - 00:16:01 CDT)
- Tesla Utilization -- NAMD 2.7b1 Ron Stubbs (Thu Aug 27 2009 - 13:06:19 CDT)
- ABF 'Xi' log output producing strange results Hugh Martin (Thu Aug 27 2009 - 10:30:22 CDT)
- Running a simulation with a protein and a sugar pellegrini (Thu Aug 27 2009 - 04:06:48 CDT)
- how to set up force parameters of a novel residue? He Yuhui (Thu Aug 27 2009 - 02:37:12 CDT)
- Postdoc position in biomolecular simulation Ivaylo Ivanov (Wed Aug 26 2009 - 16:40:02 CDT)
- question on forces / theory Ziemys, Arturas (Tue Aug 25 2009 - 22:07:07 CDT)
- fixed atoms pdb Mark M Huntress (Mon Aug 24 2009 - 17:13:20 CDT)
- multi-cluster configuration Piotr Kopta (Mon Aug 24 2009 - 16:18:42 CDT)
- Parameters for esters Jorgen Simonsen (Mon Aug 24 2009 - 11:55:08 CDT)
- About DPD «J ¦¼¯Â (Sun Aug 23 2009 - 09:52:59 CDT)
- SMD on membrane protein. Yoav Beck (Sun Aug 23 2009 - 09:04:55 CDT)
- Alignment of velocity dcd file Mert Gür (Sat Aug 22 2009 - 15:03:10 CDT)
- FATAL ERROR: ABNORMAL EOF FOUND - buffer=*0 0 0* FengXian Zheng (Fri Aug 21 2009 - 10:14:38 CDT)
- Questions from new user «J ¦¼¯Â (Thu Aug 20 2009 - 21:57:05 CDT)
- Force extension from SMD log file snoze pa (Thu Aug 20 2009 - 17:25:20 CDT)
- Re: ABF Colvars Configuration File Neelanjana Sengupta (Thu Aug 20 2009 - 09:21:41 CDT)
- unbinding SMD skill question Sangbae Lee (Wed Aug 19 2009 - 15:24:59 CDT)
- protocol to start MD jose correa (Wed Aug 19 2009 - 09:27:29 CDT)
- glibc runtime errors on BlueGeneP occur only if running the cvs code (18.08) and not namd 2.6 Vlad Cojocaru (Wed Aug 19 2009 - 05:38:47 CDT)
- About the namd tutorial err Aurum Bai (Tue Aug 18 2009 - 23:55:01 CDT)
- how to save pdb file after "moveby" command in VMD? He Yuhui (Tue Aug 18 2009 - 21:33:42 CDT)
- glibc detected : corrupted double-linked list: 0xa4657ad8 Vlad Cojocaru (Tue Aug 18 2009 - 05:15:55 CDT)
- Re: glibc detected : corrupted double-linked list: 0xa4657ad8 Vlad Cojocaru (Tue Aug 18 2009 - 05:44:58 CDT)
- Re: glibc detected : corrupted double-linked list: 0xa4657ad8 George Madalin Giambasu (Tue Aug 18 2009 - 12:05:22 CDT)
- RE: glibc detected : corrupted double-linked list: 0xa4657ad8 Cojocaru,Vlad (Tue Aug 18 2009 - 15:52:59 CDT)
- Re: glibc detected : corrupted double-linked list: 0xa4657ad8 Vlad Cojocaru (Wed Aug 19 2009 - 02:17:55 CDT)
- Re: glibc detected : corrupted double-linked list: 0xa4657ad8 Vlad Cojocaru (Wed Aug 19 2009 - 02:46:08 CDT)
- Re: glibc detected : corrupted double-linked list: 0xa4657ad8 Vlad Cojocaru (Wed Aug 19 2009 - 04:43:40 CDT)
- Re: glibc detected : corrupted double-linked list: 0xa4657ad8 George Madalin Giambasu (Tue Aug 18 2009 - 12:05:22 CDT)
- Re: glibc detected : corrupted double-linked list: 0xa4657ad8 Vlad Cojocaru (Tue Aug 18 2009 - 05:44:58 CDT)
- Berendsen, explicit water Sandra Rennebaum, Biochemisches Inst. (Tue Aug 18 2009 - 04:54:07 CDT)
- restating simuation and periodic cell conditions gurunath katagi (Tue Aug 18 2009 - 03:23:20 CDT)
- what is the charge of sulfur on thiol? He Yuhui (Mon Aug 17 2009 - 01:38:01 CDT)
- Colvars Configuration File Neelanjana Sengupta (Sat Aug 15 2009 - 02:16:19 CDT)
- (is there) a dependence of dynamics on WRAPPING satya work (Sat Aug 15 2009 - 01:33:26 CDT)
- Restarting ABF Branko (Thu Aug 13 2009 - 11:05:18 CDT)
- Re: About SMD Roman Petrenko (Thu Aug 13 2009 - 10:33:34 CDT)
- FATAL ERROR: Tried to find atom type on node other than node 0 Yoav Beck (Thu Aug 13 2009 - 09:21:38 CDT)
- Re: FATAL ERROR: Tried to find atom type on node other than node 0 yzliu (Sat Aug 15 2009 - 11:06:10 CDT)
- Re: FATAL ERROR: Tried to find atom type on node other than node 0 Yoav Beck (Mon Aug 17 2009 - 05:04:48 CDT)
- Re: FATAL ERROR: Tried to find atom type on node other than node 0 Narender Singh Maan (Mon Aug 17 2009 - 08:43:41 CDT)
- Re: FATAL ERROR: Tried to find atom type on node other than node 0 Chris Harrison (Mon Aug 17 2009 - 09:44:35 CDT)
- Minimization issue. Yoav Beck (Mon Aug 17 2009 - 10:20:41 CDT)
- Re: Minimization issue. Schreiner Eduard (Mon Aug 17 2009 - 10:33:57 CDT)
- Re: Minimization issue. Chris Harrison (Mon Aug 17 2009 - 10:43:24 CDT)
- Re: Minimization issue. Chris Harrison (Tue Aug 18 2009 - 10:51:20 CDT)
- Re: Minimization issue. Yoav Beck (Wed Aug 19 2009 - 07:11:21 CDT)
- Re: FATAL ERROR: Tried to find atom type on node other than node 0 Yoav Beck (Mon Aug 17 2009 - 05:04:48 CDT)
- Re: FATAL ERROR: Tried to find atom type on node other than node 0 yzliu (Sat Aug 15 2009 - 11:06:10 CDT)
- Bug advisory: ABF integration tool Jerome Henin (Wed Aug 12 2009 - 17:49:24 CDT)
- Kanamycin topology DimitryASuplatov (Wed Aug 12 2009 - 12:16:33 CDT)
- symmetric behavior Narender Singh Maan (Wed Aug 12 2009 - 09:16:39 CDT)
- can we control the number and distribution of solvate molecular pxq ÅÓÑ©ÇÛ (Wed Aug 12 2009 - 02:21:23 CDT)
- About "Parameterizing a Novel Residue" tutorial problem Aurum Bai (Wed Aug 12 2009 - 00:18:09 CDT)
- About SMD Yang MIngjun (Tue Aug 11 2009 - 22:11:51 CDT)
- solvate plugin with solvent other than water dalton banks (Tue Aug 11 2009 - 15:02:13 CDT)
- bonding in periodic boundary conditions d b (Tue Aug 11 2009 - 15:05:08 CDT)
- Berendsen- two baths Sandra Rennebaum, Biochemisches Inst. (Tue Aug 11 2009 - 01:55:10 CDT)
- SMD with force applied to two seperate molecules Elia Zumot (Tue Aug 11 2009 - 10:09:17 CDT)
- how to simulate a protein-ligand complex ? ydhuang2727 (Tue Aug 11 2009 - 08:29:25 CDT)
- namd-SMD constant Force missing smdatom location snoze pa (Mon Aug 10 2009 - 14:40:51 CDT)
- Steered Molecular Dynamics for more than one atom gaurav bhatti (Mon Aug 10 2009 - 13:55:10 CDT)
- Clarification regarding some finer details in ABF simulations Hugh Martin (Mon Aug 10 2009 - 12:33:47 CDT)
- combining segments d b (Mon Aug 10 2009 - 09:06:51 CDT)
- increase the temperature step by step after minimization gurunath katagi (Mon Aug 10 2009 - 00:27:03 CDT)
- how to write a command to close vmd in shell script? He Yuhui (Sun Aug 09 2009 - 22:21:34 CDT)
- On naming rules in force-field parameter files? He Yuhui (Sun Aug 09 2009 - 20:12:21 CDT)
- charm++ how to handle SMP/Multicore Bjoern Olausson (Sun Aug 09 2009 - 17:01:48 CDT)
- ABF question (free energy partition) Lei Shi (Sun Aug 09 2009 - 11:36:10 CDT)
- namd27: tclforces activate TI calculation by default George Madalin Giambasu (Sat Aug 08 2009 - 16:12:34 CDT)
- Re: Cell Data in DCD files - CHARMM compatibility Dimitar V Pachov (Fri Aug 07 2009 - 19:50:30 CDT)
- Error with GUI NAMD Energy Elia Zumot (Fri Aug 07 2009 - 16:45:23 CDT)
- SMD and Temperature control snoze pa (Fri Aug 07 2009 - 15:25:51 CDT)
- NAMD performance with 10GbE interconnect Prakash Velayutham (Fri Aug 07 2009 - 15:02:55 CDT)
- NAMD FFTW question? snoze pa (Fri Aug 07 2009 - 11:17:58 CDT)
- What is the different between "periodic boundary ,spherical harmonic boundary and cylindrical harmonic boundary conditions"? Aurum Bai (Fri Aug 07 2009 - 11:04:50 CDT)
- Would my simulation setting affect the result? About the parameter "fixedAtomsForces" wayj86 wayj86 (Fri Aug 07 2009 - 05:51:42 CDT)
- NAMDenergy: does rewrite temp files at different timesteps Neelanjana Sengupta (Fri Aug 07 2009 - 00:18:14 CDT)
- cutoffs in direct and indirect space used in PME? dimka (Thu Aug 06 2009 - 23:13:05 CDT)
- Continuing simulation after constraint failure error? Sujata Sovani (Thu Aug 06 2009 - 11:59:28 CDT)
- Re: Proteine-membrane simulation. Yoav Beck (Thu Aug 06 2009 - 07:46:05 CDT)
- Defining Temperature for Langevin for Namd restart. Amr Zeinalabideen Majul (Wed Aug 05 2009 - 14:20:15 CDT)
- Re: Defining Temperature for Langevin for Namd restart. Roman Petrenko (Wed Aug 05 2009 - 15:13:57 CDT)
- Re: Defining Temperature for Langevin for Namd restart. Gianluca Interlandi (Wed Aug 05 2009 - 16:35:14 CDT)
- Re: frozen water Oxygens Chris Harrison (Wed Aug 05 2009 - 09:01:24 CDT)
- SMD output : which col represents force, second or last snoze pa (Wed Aug 05 2009 - 11:42:42 CDT)
- SMD output : which col represents force, second or last snoze pa (Wed Aug 05 2009 - 11:25:35 CDT)
- Re: SMD output : which col represents force, second or last Roman Petrenko (Wed Aug 05 2009 - 12:05:16 CDT)
- RE: SMD output : which col represents force, second or last Sadhu, Shubho (NIH/NCI) [F] (Wed Aug 05 2009 - 12:19:27 CDT)
- Re: SMD output : which col represents force, second or last David Tanner (Wed Aug 05 2009 - 12:03:30 CDT)
- Re: SMD output : which col represents force, second or last Gianluca Interlandi (Wed Aug 05 2009 - 13:10:34 CDT)
- Re: SMD output : which col represents force, second or last Chris Harrison (Wed Aug 05 2009 - 12:27:08 CDT)
- water molecules in channel protein Narender Singh Maan (Wed Aug 05 2009 - 10:57:50 CDT)
- How to do a complex dynamics simulation ydhuang2727 (Wed Aug 05 2009 - 03:25:10 CDT)
- Simulating molecules in bulk water & VMD installation problems Vincent Su (Tue Aug 04 2009 - 14:27:38 CDT)
- SMD restrain point in NAMD snoze pa (Tue Aug 04 2009 - 11:40:05 CDT)
- frozen water Oxygens Mark M Huntress (Tue Aug 04 2009 - 11:13:12 CDT)
- Proteine-membrane simulation. Yoav Beck (Tue Aug 04 2009 - 10:08:55 CDT)
- Does Berendsen increase viscosity of water? Gianluca Interlandi (Tue Aug 04 2009 - 00:36:38 CDT)
- A script for performing calculations divided by quanta Mikhail Suyetin (Mon Aug 03 2009 - 08:26:28 CDT)
- The steps in protein and membrane simulation Narender Singh Maan (Sat Aug 01 2009 - 23:23:49 CDT)
- NAMD water sphere problem snoze pa (Fri Jul 31 2009 - 17:19:12 CDT)
- how to use ethanol as solvent in namd for MD simulations ? Wang Yf (Fri Jul 31 2009 - 04:06:55 CDT)
- compilation error "could not set locale" with intel 11.0 Vlad Cojocaru (Fri Jul 31 2009 - 03:03:53 CDT)
- Steered Molecular Dynamics gaurav bhatti (Fri Jul 31 2009 - 00:33:50 CDT)
- How to calculate free energy for conformational change Lixia Jin Day (Thu Jul 30 2009 - 16:46:07 CDT)
- CUDA Linux-x86 doesn't compile Sadhu, Shubho (NIH/NCI) [F] (Thu Jul 30 2009 - 09:06:04 CDT)
- how to generate DNA psf files? He Yuhui (Wed Jul 29 2009 - 21:04:27 CDT)
- Different ensembles in the same system Eric Perim (Wed Jul 29 2009 - 14:48:39 CDT)
- THERMODYNAMIC INTEGRATION ON in namd 2.7b1 compiled 24.07 when TCL forces active Vlad Cojocaru (Wed Jul 29 2009 - 05:03:27 CDT)
- Unable to generate PSF file due to an unparametrized component Sujata Sovani (Tue Jul 28 2009 - 16:33:09 CDT)
- (no subject) Sujata Sovani (Tue Jul 28 2009 - 17:02:30 CDT)
- FEP implementation in NAMD 2.6 vs. 2.7b1 Dan Bolintineanu (Tue Jul 28 2009 - 16:50:37 CDT)
- Equilibration "substraction" from obtained PMF from MD Branko (Tue Jul 28 2009 - 16:32:00 CDT)
- Using preprotonated structure with NAMD DimitryASuplatov (Tue Jul 28 2009 - 09:48:18 CDT)
- PLUMED release 1.1.0 available Massimiliano Bonomi (Tue Jul 28 2009 - 03:12:27 CDT)
- use tclForce and tclBC together? yun luo (Mon Jul 27 2009 - 20:14:45 CDT)
- error running namd Bernardo Sosa Padilla Araujo (Mon Jul 27 2009 - 16:37:17 CDT)
- hydroxyls in phosphate group collapsing Yvonne.Westermaier_at_unige.ch (Mon Jul 27 2009 - 09:41:20 CDT)
- Group forces in tclForces Benjamin Bouvier (Mon Jul 27 2009 - 06:02:12 CDT)
- Re: An outlier appear on the curve of RMSD wayj86 wayj86 (Sun Jul 26 2009 - 20:42:13 CDT)
- How to set magnitude of cellBasisVector? Aurum Bai (Fri Jul 24 2009 - 00:52:19 CDT)
- An outlier appear on the curve of RMSD wayj86 wayj86 (Thu Jul 23 2009 - 22:37:04 CDT)
- how to run namd2.7b1 on multiple nodes Roman Petrenko (Thu Jul 23 2009 - 17:48:19 CDT)
- NAMD documentation regarding compiling Thomas C. Bishop (Thu Jul 23 2009 - 15:25:19 CDT)
- RescaleFreq of temperature =1? Mikhail Suyetin (Thu Jul 23 2009 - 09:48:54 CDT)
- NAMD CUDA on dual Nvidia 295 GPUs David Chalmers (Thu Jul 23 2009 - 07:20:34 CDT)
- Re: NAMD CUDA on dual Nvidia 295 GPUs Axel Kohlmeyer (Thu Jul 23 2009 - 08:04:42 CDT)
- RE: NAMD CUDA on dual Nvidia 295 GPUs Sadhu, Shubho (NIH/NCI) [F] (Thu Jul 23 2009 - 09:11:48 CDT)
- Re: RE: NAMD CUDA on dual Nvidia 295 GPUs Axel Kohlmeyer (Thu Jul 23 2009 - 10:02:45 CDT)
- RE: RE: NAMD CUDA on dual Nvidia 295 GPUs Sadhu, Shubho (NIH/NCI) [F] (Thu Jul 23 2009 - 12:14:42 CDT)
- RE: RE: NAMD CUDA on dual Nvidia 295 GPUs Axel Kohlmeyer (Thu Jul 23 2009 - 12:28:24 CDT)
- NAMD CUDA performance degradation Thomas C. Bishop (Thu Jul 23 2009 - 14:31:10 CDT)
- Re: NAMD CUDA performance degradation Axel Kohlmeyer (Thu Jul 23 2009 - 15:19:16 CDT)
- Re: RE: NAMD CUDA on dual Nvidia 295 GPUs Axel Kohlmeyer (Thu Jul 23 2009 - 10:02:45 CDT)
- maximum residues using AMBER parm with NAMD benc_at_bsc.es (Wed Jul 22 2009 - 05:09:17 CDT)
- NAMD installation Bernardo Sosa Padilla Araujo (Wed Jul 22 2009 - 17:33:15 CDT)
- NAMD 2.7b1 with APBS/iAPBS Bjoern Olausson (Wed Jul 22 2009 - 02:56:07 CDT)
- Measuring the molarity Rabab Toubar (Wed Jul 22 2009 - 15:16:58 CDT)
- inconsistence in NAMD and AMBER energy Yi Shang (Mon Jul 20 2009 - 18:31:47 CDT)
- Re: inconsistence in NAMD and AMBER energy Goutham (Tue Jul 21 2009 - 01:13:48 CDT)
- Re: inconsistence in NAMD and AMBER energy Floris Buelens (Tue Jul 21 2009 - 02:11:51 CDT)
- Re: inconsistence in NAMD and AMBER energy Thomas C. Bishop (Tue Jul 21 2009 - 09:33:35 CDT)
- Re: inconsistence in NAMD and AMBER energy Yi Shang (Tue Jul 21 2009 - 09:56:04 CDT)
- Re: inconsistence in NAMD and AMBER energy Thomas C. Bishop (Tue Jul 21 2009 - 10:14:28 CDT)
- Re: inconsistence in NAMD and AMBER energy Yi Shang (Tue Jul 21 2009 - 10:22:45 CDT)
- Re: inconsistence in NAMD and AMBER energy: AMBER truncted octahedron Vlad Cojocaru (Tue Jul 21 2009 - 11:08:40 CDT)
- Re: inconsistence in NAMD and AMBER energy: AMBER truncted octahedron Thomas C. Bishop (Tue Jul 21 2009 - 11:30:35 CDT)
- Re: inconsistence in NAMD and AMBER energy: AMBER truncted octahedron Vlad Cojocaru (Wed Jul 22 2009 - 04:44:45 CDT)
- Re: inconsistence in NAMD and AMBER energy Thomas C. Bishop (Tue Jul 21 2009 - 11:11:39 CDT)
- Re: inconsistence in NAMD and AMBER energy Floris Buelens (Tue Jul 21 2009 - 10:57:41 CDT)
- Re: inconsistence in NAMD and AMBER energy Yi Shang (Tue Jul 21 2009 - 11:04:18 CDT)
- Re: inconsistence in NAMD and AMBER energy George Madalin Giambasu (Tue Jul 21 2009 - 11:27:03 CDT)
- Re: inconsistence in NAMD and AMBER energy Thomas C. Bishop (Tue Jul 21 2009 - 09:33:35 CDT)
- ABF tutorial sudipta (Mon Jul 20 2009 - 08:57:54 CDT)
- on NAMD simulation of DNA translocation through nanopores yuhuihe_at_ime.pku.edu.cn (Sun Jul 19 2009 - 07:27:55 CDT)
- about compile namd2.7 liupeng012 (Sun Jul 19 2009 - 05:58:05 CDT)
- CPU USAGE mahmoud mirzaei (Sat Jul 18 2009 - 11:14:10 CDT)
- Re: CPU USAGE Axel Kohlmeyer (Sat Jul 18 2009 - 11:50:25 CDT)
- Re: CPU USAGE mahmoud mirzaei (Sat Jul 18 2009 - 23:07:26 CDT)
- RE: CPU USAGE JC Gumbart (Sun Jul 19 2009 - 00:16:30 CDT)
- RE: CPU USAGE mahmoud (Sun Jul 19 2009 - 04:15:08 CDT)
- Re: CPU USAGE Benjamin Bouvier (Sun Jul 19 2009 - 04:51:32 CDT)
- Re: CPU USAGE Nicholas M Glykos (Sun Jul 19 2009 - 06:57:56 CDT)
- Re: CPU USAGE Axel Kohlmeyer (Sun Jul 19 2009 - 11:15:14 CDT)
- Re: CPU USAGE mahmoud mirzaei (Sat Jul 18 2009 - 23:07:26 CDT)
- Re: CPU USAGE Axel Kohlmeyer (Sat Jul 18 2009 - 11:50:25 CDT)
- NAMD 2.7b1 Jianhui Tian (Fri Jul 17 2009 - 10:52:28 CDT)
- NAMD hanging on GPU Sadhu, Shubho (NIH/NCI) [F] (Fri Jul 17 2009 - 08:00:21 CDT)
- Reassign Temp during the Production Run twshen (Thu Jul 16 2009 - 12:04:03 CDT)
- Grid Forces documentation Hugh Martin (Thu Jul 16 2009 - 08:02:04 CDT)
- VMD-Installation problems jose correa (Wed Jul 15 2009 - 19:16:35 CDT)
- molecule jumps from one site to the other? uu zhu (Mon Jul 13 2009 - 21:11:52 CDT)
- Implementation of graphite walls Sabine Leroch (Mon Jul 13 2009 - 07:36:05 CDT)
- Fwd: one atom off in the minimization result Chris Harrison (Sun Jul 12 2009 - 18:23:10 CDT)
- Re: Tried to find atom type on node other than node 0 Narender Singh Maan (Mon Jul 13 2009 - 10:46:47 CDT)
- Bad global exclusion count Yogesh Aher (Mon Jul 13 2009 - 05:57:18 CDT)
- Fwd: PROBLEM OF INSTALLATION OF NAMD ipsita basu (Sun Jul 12 2009 - 23:28:30 CDT)
- Fwd: Minimization problem of a protein-DNA complex with namd Chris Harrison (Sun Jul 12 2009 - 18:23:40 CDT)
- one atom off in the minimization result mgssal (Sun Jul 12 2009 - 03:22:46 CDT)
- Minimization problem of a protein-DNA complex with namd sudipta (Sun Jul 12 2009 - 02:21:36 CDT)
- Fwd: 99999999.9999 as vander waals energy Chris Harrison (Sat Jul 11 2009 - 19:38:30 CDT)
- Simulating Protonated base pairs of RNA Monika Sharma (Sat Jul 11 2009 - 07:07:29 CDT)
- pdbalias for PO4 residue gurunath katagi (Sat Jul 11 2009 - 01:09:29 CDT)
- 99999999.9999 as vander waals energy Uma Mageshwari (Sat Jul 11 2009 - 00:18:19 CDT)
- SMD working only at high velocity Elia Zumot (Fri Jul 10 2009 - 13:20:33 CDT)
- Intel 11 compilers Xavier Deupi (Fri Jul 10 2009 - 08:52:58 CDT)
- protein folding doty alexiou (Fri Jul 10 2009 - 03:00:37 CDT)
- bug or custom? BIN ZHANG (Thu Jul 09 2009 - 13:00:44 CDT)
- Fwd: Tried to find atom type on node other than node 0 Chris Harrison (Thu Jul 09 2009 - 09:45:23 CDT)
- Tried to find atom type on node other than node 0 Narender Singh Maan (Thu Jul 09 2009 - 09:00:44 CDT)
- Re: Generation of .psf file of DNA Jian Liu (Thu Jul 09 2009 - 07:43:21 CDT)
- Re: namd hangs or exits with segmentation faults on opteron cluster with infiniband Vlad Cojocaru (Thu Jul 09 2009 - 06:59:31 CDT)
- Another strange error: MStream checksums do not agree Vlad Cojocaru (Thu Jul 09 2009 - 03:05:13 CDT)
- Generation of .psf file of DNA sudipta (Thu Jul 09 2009 - 01:53:25 CDT)
- bicarbonate parameters Brian R Novak (Wed Jul 08 2009 - 13:31:28 CDT)
- FATAL ERROR: Sorry, combined TI and FEP is not implemented Vlad Cojocaru (Wed Jul 08 2009 - 05:41:00 CDT)
- LES problem Irene Newhouse (Tue Jul 07 2009 - 00:30:50 CDT)
- Fatal Error Help Goutham (Mon Jul 06 2009 - 16:10:18 CDT)
- Translocation problem while attempting to use ABF Hugh Martin (Mon Jul 06 2009 - 10:39:38 CDT)
- END: No log file Luis Agullo (LAB) (Mon Jul 06 2009 - 09:56:15 CDT)
- No log file Luis Agullo (LAB) (Mon Jul 06 2009 - 08:41:14 CDT)
- protein collapsing problem ydhuang2727 (Sun Jul 05 2009 - 20:12:38 CDT)
- Re: Re: namd2.7b1 slower with openmpi 1.3.2 than namd2.6 withopenmpi 1.2.6 liupeng012 (Sat Jul 04 2009 - 21:17:15 CDT)
- about psfgen emilia.l.wu (Sat Jul 04 2009 - 08:59:44 CDT)
- implicit solvent model in NAMD? Yinglong Miao (Fri Jul 03 2009 - 15:18:17 CDT)
- namd hangs or exits with segmentation faults on opteron cluster with infiniband Vlad Cojocaru (Fri Jul 03 2009 - 08:16:28 CDT)
- Hardware for NAMD / VMD machine Olve Peersen (Fri Jul 03 2009 - 01:26:11 CDT)
- ERROR! Explicit exclusions or fluctuating charges not supported, atom ignored. emilia wu (Thu Jul 02 2009 - 18:35:32 CDT)
- NAMD_ti.pl Philip Fowler (Wed Jul 01 2009 - 06:45:31 CDT)
- Par and Top files for BCL Kovács, Sándor Ádám (Thu Jul 02 2009 - 12:08:08 CDT)
- namd2.7b1 slower with openmpi 1.3.2 than namd2.6 with openmpi 1.2.6 Vlad Cojocaru (Thu Jul 02 2009 - 10:41:23 CDT)
- nose-hoover David A. Horita (Wed Jul 01 2009 - 10:36:30 CDT)
- NAMD_ti.pl Philip Fowler (Wed Jul 01 2009 - 07:50:26 CDT)
- NAMD Installation mahmoud (Wed Jul 01 2009 - 02:53:51 CDT)
- location of the SMD source code Liang (Tue Jun 30 2009 - 13:17:48 CDT)
- Hi,all, the parameters for Strain uu zhu (Tue Jun 30 2009 - 01:32:26 CDT)
- GPGPU Programming summer school at University of Tennessee, Aug 10-14. Axel Kohlmeyer (Mon Jun 29 2009 - 14:43:11 CDT)
- namd cvs 26.06.09, tcl 8.5, loadcoords Vlad Cojocaru (Mon Jun 29 2009 - 09:10:46 CDT)
- Modeling of Gramicidin A Jian Liu (Mon Jun 29 2009 - 08:08:41 CDT)
- Protein collpasing problem! ydhuang2727 (Mon Jun 29 2009 - 01:12:47 CDT)
- defenestrate Peter Freddolino (Sun Jun 28 2009 - 15:20:11 CDT)
- unsubscribe Anna Blice-Baum (Sun Jun 28 2009 - 14:40:10 CDT)
- unsubscribe wavedalla\_at_libero\.it (Sun Jun 28 2009 - 09:49:09 CDT)
- Can I use another solvent rather than TI3P model in namd for MD simulations ? Wang Yf (Sat Jun 27 2009 - 22:30:04 CDT)
- the recent flood of unsubscribe requests Axel Kohlmeyer (Sat Jun 27 2009 - 10:07:28 CDT)
- unsubscribe Ariovaldo de Souza Junior (Sat Jun 27 2009 - 09:25:57 CDT)
- unsubscribe C. Denise Enekwa (Sat Jun 27 2009 - 06:41:19 CDT)
- unsubscribe Nd S (Sat Jun 27 2009 - 00:41:38 CDT)
- unsubscribe Vinit Rege (Fri Jun 26 2009 - 22:27:45 CDT)
- unsubscribe Hatley, Jade M (Fri Jun 26 2009 - 19:02:48 CDT)
- colvars: Error: undefined output or restart file. Bonnie Merchant (Fri Jun 26 2009 - 13:41:42 CDT)
- My protein went out of the water box in SMD. Would it have a bad effect on the result? wayj86 wayj86 (Fri Jun 26 2009 - 03:02:46 CDT)
- Grid Forces gbellesia_at_chem.ucsb.edu (Thu Jun 25 2009 - 15:31:19 CDT)
- Does NAMD have any capability to assign coordiantes to novel sequences? Amr Zeinalabideen Majul (Thu Jun 25 2009 - 10:34:43 CDT)
- protein collapsing problem! ydhuang2727 (Thu Jun 25 2009 - 00:08:29 CDT)
- regarding positioning of protein molecule prasun kumar (Wed Jun 24 2009 - 17:39:15 CDT)
- bugfixes in the colvars module (ABF, metadynamics etc.) Giacomo Fiorin (Wed Jun 24 2009 - 16:00:27 CDT)
- Re: launch NAMD from tcl script J Liu (Wed Jun 24 2009 - 08:58:47 CDT)
- launch NAMD from tcl script Floris Buelens (Wed Jun 24 2009 - 06:55:06 CDT)
- Total energy of a residue Mert Gür (Tue Jun 23 2009 - 10:08:12 CDT)
- Re: 2.7b metadynamics ::hBond component :: folding of a single helix in water Ali Emileh (Mon Jun 22 2009 - 14:23:57 CDT)
- Pair interaction : Energy values are zero Navendu bhatnagar (Sun Jun 21 2009 - 16:01:45 CDT)
- FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3 gurunath katagi (Sat Jun 20 2009 - 12:59:51 CDT)
- VMD/NAMD two identical molecules solvate in a water sphere David Jiang (Sat Jun 20 2009 - 11:02:49 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere Eric H. Lee (Sat Jun 20 2009 - 12:46:25 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere Joshua Adelman (Sat Jun 20 2009 - 12:21:49 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere David Jiang (Tue Jun 23 2009 - 10:27:07 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere Peter Freddolino (Tue Jun 23 2009 - 11:17:54 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere David Jiang (Tue Jun 23 2009 - 11:34:04 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere Peter Freddolino (Tue Jun 23 2009 - 12:06:21 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere David Jiang (Tue Jun 23 2009 - 14:02:48 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere Peter Freddolino (Tue Jun 23 2009 - 14:11:15 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere David Jiang (Tue Jun 23 2009 - 10:27:07 CDT)
- Developing a neutral arginine patch in a topology file urmit shah (Fri Jun 19 2009 - 17:54:19 CDT)
- Re: Reassign temp bay__gulf618_at_sina.com (Wed Jun 17 2009 - 20:44:15 CDT)
- Reassign temp Marcelo Puiatti (Wed Jun 17 2009 - 15:27:18 CDT)
- collective variables Jarrod Nickel (Wed Jun 17 2009 - 11:07:26 CDT)
- How is dG caluclated from dE during FEP? Michael Thomas (Wed Jun 17 2009 - 06:51:31 CDT)
- Re: Re: Thermodynamic integration script - where is it? Floris Buelens (Tue Jun 16 2009 - 02:37:44 CDT)
- to run NAMD on a PC Lixia Jin Day (Mon Jun 15 2009 - 12:59:08 CDT)
- need advices for running NAMD efficiently. Lixia Jin Day (Mon Jun 15 2009 - 12:44:55 CDT)
- Postdoc position in biomolecular simulation Ivaylo, Ivanov (Sat Jun 13 2009 - 02:08:07 CDT)
- Postdoc position in biomolecular simulation Ivaylo, Ivanov (Sat Jun 13 2009 - 01:37:55 CDT)
- Histamine topology file r charbel maroun (Fri Jun 12 2009 - 11:32:35 CDT)
- regarding psfgen algorithm prasun kumar (Fri Jun 12 2009 - 03:22:04 CDT)
- What decides the pulling direction in SMD? Àîè (Fri Jun 12 2009 - 02:35:15 CDT)
- Force Constant Units Kamilla Kopec (Wed Jun 10 2009 - 12:08:24 CDT)
- compile NAMD with TCP and SMP sudipta (Wed Jun 10 2009 - 00:19:18 CDT)
- ABF simulations Sumanth Jamadagni (Tue Jun 09 2009 - 21:08:10 CDT)
- question about repeating output text ershela.durresi_at_yale.edu (Tue Jun 09 2009 - 05:58:20 CDT)
- How to set the parameters for two different baths in one molecule? uu zhu (Mon Jun 08 2009 - 20:14:36 CDT)
- Bug advisory: RMSD and ABF Jerome Henin (Mon Jun 08 2009 - 17:55:10 CDT)
- Problem namd2 and mpich2 sudipta (Mon Jun 08 2009 - 01:40:58 CDT)
- Read DCD file in Java Kejun (Kevin) Dong (Sat Jun 06 2009 - 00:39:27 CDT)
- regarding protein-protein interaction prasun kumar (Fri Jun 05 2009 - 02:51:37 CDT)
- Re: regarding protein-protein interaction Marcin Krol (Fri Jun 05 2009 - 03:23:13 CDT)
- Re: regarding protein-protein interaction L. Michel Espinoza-Fonseca (Fri Jun 05 2009 - 03:19:43 CDT)
- Re: regarding protein-protein interaction Benjamin Bouvier (Fri Jun 05 2009 - 03:50:21 CDT)
- Re: regarding protein-protein interaction Joshua Adelman (Fri Jun 05 2009 - 10:41:44 CDT)
- protein folding cg doty alexiou (Fri Jun 05 2009 - 01:21:16 CDT)
- Please disregard the spam "Lei sent you private photos on Tagged :)" Lei Shi (Thu Jun 04 2009 - 17:04:05 CDT)
- tclforces and minimization Roman Petrenko (Thu Jun 04 2009 - 16:42:27 CDT)
- abf with colvars example David A. Horita (Thu Jun 04 2009 - 12:53:20 CDT)
- Charmrun/INTEL MAC/2.7 Grabe, Michael David (Thu Jun 04 2009 - 09:21:21 CDT)
- Exclusions and CUDA Benjamin Bouvier (Thu Jun 04 2009 - 03:40:22 CDT)
- NAMD on GPU xiaojing gong (Thu Jun 04 2009 - 02:53:18 CDT)
- namd 2.7b1 on infiniband about the error : stack Traceback liupeng012 (Thu Jun 04 2009 - 00:10:32 CDT)
- Measuring protein diffusion: results too small? Stephen Hicks (Wed Jun 03 2009 - 16:49:03 CDT)
- lamboot -v nodelist Yogesh Aher (Wed Jun 03 2009 - 09:49:15 CDT)
- compile namd2.7b1 on infiniband liupeng012 (Tue Jun 02 2009 - 21:43:16 CDT)
- Namd lite Goutham (Tue Jun 02 2009 - 19:54:21 CDT)
- 2.7b metadynamics ::alpha module :: folding of a single helix in water Ali Emileh (Tue Jun 02 2009 - 18:39:25 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Giacomo Fiorin (Fri Jun 05 2009 - 10:53:48 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Ali Emileh (Tue Jun 09 2009 - 11:52:19 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Giacomo Fiorin (Tue Jun 09 2009 - 12:24:39 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Ali Emileh (Tue Jun 09 2009 - 18:02:12 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Giacomo Fiorin (Wed Jun 10 2009 - 08:57:38 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Ali Emileh (Wed Jul 22 2009 - 21:18:11 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Giacomo Fiorin (Mon Jul 27 2009 - 11:52:44 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Ali Emileh (Tue Jun 09 2009 - 11:52:19 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Giacomo Fiorin (Fri Jun 05 2009 - 10:53:48 CDT)
- Fwd: RESP and CHARMM r charbel maroun (Tue Jun 02 2009 - 08:35:17 CDT)
- IMD, Hostname and Port Nano Group (Tue Jun 02 2009 - 07:40:01 CDT)
- force output of pairInteraction BIN ZHANG (Mon Jun 01 2009 - 17:20:07 CDT)
- Rescale Temperature when velocity of COM is not zero Fred (Rui FENG) (Mon Jun 01 2009 - 15:12:05 CDT)
- Re: Thermodynamic integration script - where is it? Lela Vukovic (Mon Jun 01 2009 - 12:52:38 CDT)
- FATAL ERROR: Bad global exclusion count! KIRTANA S (Mon Jun 01 2009 - 12:37:38 CDT)
- flipdcd Michael Kreim (Sat May 30 2009 - 07:12:34 CDT)
- Regd: Error KIRTANA S (Sun May 31 2009 - 22:52:15 CDT)
- regd: my parameter file KIRTANA S (Fri May 29 2009 - 16:05:26 CDT)
- Regd :parameter file KIRTANA S (Fri May 29 2009 - 15:56:04 CDT)
- visualize energy on a structure Michael Zimmermann (Fri May 29 2009 - 12:20:24 CDT)
- using amber topology and parameter files in NAMD KIRTANA S (Fri May 29 2009 - 12:16:54 CDT)
- water molecules "collapse" during equilibration enz1+_at_pitt.edu (Fri May 29 2009 - 11:38:06 CDT)
- FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE Yogesh Aher (Fri May 29 2009 - 09:34:13 CDT)
- electric field along z-direction Roman Petrenko (Wed May 27 2009 - 16:21:27 CDT)
- unknown path type LSN ÖÜÎIJý (Tue May 26 2009 - 07:48:49 CDT)
- TMD for moving ion across membrane yun luo (Mon May 25 2009 - 12:10:59 CDT)
- Software to Mutate DNA sunita gupta (Mon May 25 2009 - 08:39:51 CDT)
- NAMD 2.7b1 running & performance issues Marius Micluta (Mon May 25 2009 - 06:13:07 CDT)
- Force on multiple atoms in ABF Mert Gür (Sun May 24 2009 - 11:26:16 CDT)
- Postdoctoral Position in Scientific Computing VMD NAMD Postdoc Position (Sat May 23 2009 - 13:41:27 CDT)
- Offset for frame ids in dcd trajectory DimitryASuplatov (Sat May 23 2009 - 11:11:09 CDT)
- Warning: Not all atoms have unique coordinates Jarrod Nickel (Fri May 22 2009 - 14:08:34 CDT)
- GridForces methodology in NAMD 2.7b1 Giovanni Bellesia (Fri May 22 2009 - 13:26:16 CDT)
- triazol parameters Ziemys, Arturas (Thu May 21 2009 - 16:01:53 CDT)
- NAMD2.6 - 1D Periodic Boundary and PME - FATAL ERROR: PME requires periodic boundary conditions. Greg Guthe (Thu May 21 2009 - 15:32:47 CDT)
- selectively write atom coordinates on-the-fly Vasudevan V (Thu May 21 2009 - 11:29:35 CDT)
- Harmonically constrained simulations Sumanth Jamadagni (Thu May 21 2009 - 10:00:13 CDT)
- calculating energy for large log files gurunath katagi (Thu May 21 2009 - 02:30:40 CDT)
- Fw: NAMD 2.7b1 running problem bay__gulf618_at_sina.com (Wed May 20 2009 - 20:10:15 CDT)
- NAMD Tuning page on the wiki vs. NAMD/CUDA Dow_Hurst (Wed May 20 2009 - 18:09:21 CDT)
- tmao molecule Vasudevan V (Wed May 20 2009 - 09:43:40 CDT)
- Free energy of conformational change Branko (Wed May 20 2009 - 06:15:57 CDT)
- NAMD 2.7b1 running problem ÖÜÎIJý (Wed May 20 2009 - 05:19:19 CDT)
- calculating forces from dcd trajectory BIN ZHANG (Wed May 20 2009 - 02:18:26 CDT)
- namd-openmosix jose correa (Tue May 19 2009 - 07:29:49 CDT)
- REMD on AIX5.3 Florian Janetzko (Tue May 19 2009 - 06:44:34 CDT)
- How to minimize our model by SD using namd Ahmad Firoz (Tue May 19 2009 - 00:33:01 CDT)
- Periodic Forcing Functions Rick Calloway (Mon May 18 2009 - 16:50:42 CDT)
- NAMD infiniband performance Guanglei Cui (Mon May 18 2009 - 16:10:55 CDT)
- Re: NAMD infiniband performance Lev Lafayette (Tue May 19 2009 - 01:31:47 CDT)
- Re: NAMD infiniband performance Guanglei Cui (Tue May 19 2009 - 08:56:00 CDT)
- Re: NAMD infiniband performance Axel Kohlmeyer (Tue May 19 2009 - 10:00:11 CDT)
- Re: NAMD infiniband performance Guanglei Cui (Tue May 19 2009 - 11:06:09 CDT)
- Re: NAMD infiniband performance Guanglei Cui (Tue May 19 2009 - 11:04:39 CDT)
- Re: NAMD infiniband performance Axel Kohlmeyer (Tue May 19 2009 - 17:13:50 CDT)
- Re: NAMD infiniband performance Guanglei Cui (Mon Jun 01 2009 - 15:15:23 CDT)
- Re: NAMD infiniband performance Axel Kohlmeyer (Mon Jun 01 2009 - 15:54:17 CDT)
- Re: NAMD infiniband performance Guanglei Cui (Mon Jun 01 2009 - 21:27:07 CDT)
- Re: NAMD infiniband performance Axel Kohlmeyer (Mon Jun 01 2009 - 21:58:49 CDT)
- Re: NAMD infiniband performance Guanglei Cui (Tue May 19 2009 - 08:56:00 CDT)
- Re: NAMD infiniband performance Lev Lafayette (Tue May 19 2009 - 01:31:47 CDT)
- about limitdist cong chen (Mon May 18 2009 - 06:11:48 CDT)
- Error running NAMD on CUDA jani sahil (Mon May 18 2009 - 03:34:11 CDT)
- the external electric field vector uu zhu (Mon May 18 2009 - 01:56:29 CDT)
- exclude 1-2 doty alexiou (Fri May 15 2009 - 01:55:09 CDT)
- charm++ build problem Yogesh (Thu May 14 2009 - 08:24:42 CDT)
- TMD biasing Felipe Merino (Thu May 14 2009 - 06:23:23 CDT)
- peptides on surface Jorgen Simonsen (Wed May 13 2009 - 13:16:51 CDT)
- Need help to generate ubq-get-energy.conf Mert Gür (Wed May 13 2009 - 10:06:55 CDT)
- Re: Need help to generate ubq-get-energy.conf Peter Freddolino (Wed May 13 2009 - 12:03:55 CDT)
- Re: Need help to generate ubq-get-energy.conf Mert Gür (Wed May 13 2009 - 15:49:24 CDT)
- Re: Need help to generate ubq-get-energy.conf Peter Freddolino (Wed May 13 2009 - 15:55:29 CDT)
- Re: Need help to generate ubq-get-energy.conf Mert Gür (Thu May 14 2009 - 02:01:27 CDT)
- Re: Need help to generate ubq-get-energy.conf Eric H. Lee (Thu May 14 2009 - 02:52:20 CDT)
- Re: Need help to generate ubq-get-energy.conf Mert Gür (Thu May 14 2009 - 05:43:46 CDT)
- Re: Need help to generate ubq-get-energy.conf Peter Freddolino (Thu May 14 2009 - 10:33:10 CDT)
- Re: Need help to generate ubq-get-energy.conf Mert Gür (Thu May 14 2009 - 13:00:57 CDT)
- Re: Need help to generate ubq-get-energy.conf Peter Freddolino (Thu May 14 2009 - 11:33:57 CDT)
- Re: Need help to generate ubq-get-energy.conf Mert Gür (Wed May 13 2009 - 15:49:24 CDT)
- Re: Need help to generate ubq-get-energy.conf Peter Freddolino (Wed May 13 2009 - 12:03:55 CDT)
- Make NAMD2.7b1 with cuda bug? Lev Lafayette (Tue May 12 2009 - 22:48:04 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Roman Petrenko (Wed May 13 2009 - 08:56:02 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Charles Taylor (Wed May 13 2009 - 09:29:27 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Jim Phillips (Wed May 13 2009 - 11:58:30 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Gengbin Zheng (Wed May 13 2009 - 12:09:03 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Jim Phillips (Wed May 13 2009 - 13:41:29 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Gengbin Zheng (Wed May 13 2009 - 15:47:44 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Lev Lafayette (Thu May 14 2009 - 01:12:41 CDT)
- Re: Make NAMD2.7b1 with cuda bug? jani sahil (Fri May 15 2009 - 03:00:35 CDT)
- Re: Make NAMD2.7b1 with cuda bug? jani sahil (Fri May 15 2009 - 04:23:17 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Roman Petrenko (Wed May 13 2009 - 08:56:02 CDT)
- changing protonation states for a pdb with more than a single polypeptide Elia Zomot (Tue May 12 2009 - 18:47:41 CDT)
- PSF file KIRTANA S (Tue May 12 2009 - 14:29:05 CDT)
- exclude 1-2 or 1-4? doty alexiou (Tue May 12 2009 - 09:56:31 CDT)
- Which compiler-suite was used... Bjoern Olausson (Tue May 12 2009 - 07:26:00 CDT)
- Asymmetric water molecule found Jorgen Simonsen (Tue May 12 2009 - 05:00:45 CDT)
- namd-cuda-intel vs. namd-intel Roman Petrenko (Tue May 12 2009 - 00:32:58 CDT)
- Re: namd-cuda-intel vs. namd-intel Axel Kohlmeyer (Tue May 12 2009 - 06:24:04 CDT)
- Calculating displacement in a system with periodic boundary Fred (Rui FENG) (Mon May 11 2009 - 23:26:21 CDT)
- Re: Calculating displacement in a system with periodic boundary Joshua Adelman (Mon May 11 2009 - 23:44:23 CDT)
- Re: Calculating displacement in a system with periodic boundary Eric H. Lee (Mon May 11 2009 - 23:49:25 CDT)
- Re: Calculating displacement in a system with periodic boundary Fred (Rui FENG) (Tue May 12 2009 - 01:07:22 CDT)
- Re: Calculating displacement in a system with periodic boundary Eric H. Lee (Tue May 12 2009 - 01:15:56 CDT)
- Re: Calculating displacement in a system with periodic boundary Fred (Rui FENG) (Tue May 12 2009 - 01:37:58 CDT)
- Re: Calculating displacement in a system with periodic boundary BIN ZHANG (Tue May 12 2009 - 02:25:48 CDT)
- Re: Calculating displacement in a system with periodic boundary Fred (Rui FENG) (Tue May 12 2009 - 02:52:49 CDT)
- Re: Calculating displacement in a system with periodic boundary Fred (Rui FENG) (Tue May 12 2009 - 01:07:22 CDT)
- FEP on 2.7b1 Christopher Hartshorn (Mon May 11 2009 - 15:38:37 CDT)
- collective variable space PMF, including biasing potential terms? Sebastian Stolzenberg (Wed May 13 2009 - 14:48:05 CDT)
- Re: collective variable space PMF, including biasing potential terms? Jerome Henin (Wed May 13 2009 - 16:23:49 CDT)
- Re: collective variable space PMF, including biasing potential terms? Roman Petrenko (Wed May 13 2009 - 17:00:49 CDT)
- Re: collective variable space PMF, including biasing potential terms? Chris Chipot (Wed May 13 2009 - 17:37:04 CDT)
- Re: collective variable space PMF, including biasing potential terms? Roman Petrenko (Wed May 13 2009 - 17:45:29 CDT)
- Re: collective variable space PMF, including biasing potential terms? Axel Kohlmeyer (Wed May 13 2009 - 17:52:30 CDT)
- Re: collective variable space PMF, including biasing potential terms? Chris Chipot (Wed May 13 2009 - 18:16:54 CDT)
- NAMD 2.7b1: metadynamics+tclForces => "... design error, GlobalMasterServer..." Sebastian Stolzenberg (Thu May 14 2009 - 16:41:16 CDT)
- Re: NAMD 2.7b1: metadynamics+tclForces => "... design error, GlobalMasterServer..." Giacomo Fiorin (Thu May 14 2009 - 19:23:19 CDT)
- mercury ion parameters? Sebastian Stolzenberg (Sat May 23 2009 - 11:12:04 CDT)
- Re: collective variable space PMF, including biasing potential terms? Giacomo Fiorin (Wed May 13 2009 - 16:38:56 CDT)
- Re: collective variable space PMF, including biasing potential terms? Jerome Henin (Wed May 13 2009 - 16:23:49 CDT)
- collective variable space PMF, including biasing potential terms? Sebastian Stolzenberg (Wed May 13 2009 - 14:48:05 CDT)
- SiCortex with Pathscale Christopher Hartshorn (Sat May 09 2009 - 19:52:29 CDT)
- ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Mon May 11 2009 - 07:15:42 CDT)
- ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Mon May 11 2009 - 07:38:38 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Peter Freddolino (Mon May 11 2009 - 08:09:40 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Mon May 11 2009 - 08:20:29 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Peter Freddolino (Mon May 11 2009 - 12:11:57 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Tue May 12 2009 - 03:02:45 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Peter Freddolino (Tue May 12 2009 - 06:41:29 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Thu May 14 2009 - 04:02:29 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Peter Freddolino (Thu May 14 2009 - 10:19:28 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Roberta Rostagno (Fri May 15 2009 - 02:19:09 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Peter Freddolino (Fri May 15 2009 - 05:54:11 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Wed May 20 2009 - 09:44:02 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Peter Freddolino (Wed May 20 2009 - 09:59:45 CDT)
- ERROR: Stray PME grid charges detected roberta.rostagno (Mon May 25 2009 - 04:34:11 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Mon May 11 2009 - 08:20:29 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Peter Freddolino (Mon May 11 2009 - 08:09:40 CDT)
- lipid bi-layer and SiO2 Raul Araya (Fri May 08 2009 - 14:36:41 CDT)
- NAMD with CUDA Prakash Velayutham (Thu May 07 2009 - 13:06:04 CDT)
- HW - HW IN PARAMETER FILES Jorgen Simonsen (Thu May 07 2009 - 06:17:19 CDT)
- water models and some questions fett_at_vtr.net (Thu May 07 2009 - 06:02:39 CDT)
- running namd2.7 problem ydhuang2727 (Thu May 07 2009 - 01:23:46 CDT)
- force-field for cy3, cy5 dyes Roman Petrenko (Wed May 06 2009 - 19:26:54 CDT)
- (no subject) Wang,Ying (Wed May 06 2009 - 13:50:12 CDT)
- diffusion / fex peptide problem Benjamin Stauch (Wed May 06 2009 - 10:24:16 CDT)
- fatal error: tried to assign bond index before all parameter files were read Jorgen Simonsen (Wed May 06 2009 - 05:36:16 CDT)
- umbrella sampling script Hyundeok Song (Tue May 05 2009 - 17:30:28 CDT)
- Langevin damping coefficient Gianluca Interlandi (Tue May 05 2009 - 16:49:30 CDT)
- Postdoc position in computational biophysics and nanotechnology Aleksei Aksimentiev (Tue May 05 2009 - 14:34:04 CDT)
- Re: Value for "firsttimestep" when restarting MD Bjoern Olausson (Tue May 05 2009 - 12:45:56 CDT)
- Value for "firsttimestep" when restarting MD Bjoern Olausson (Tue May 05 2009 - 09:50:42 CDT)
- regarding simulation prasun kumar (Tue May 05 2009 - 08:48:00 CDT)
- DCOLVARS_DEBUG George Madalin Giambasu (Mon May 04 2009 - 22:49:17 CDT)
- truncated octahedral daniel aguayo (Mon May 04 2009 - 20:21:37 CDT)
- geomtery optimization with namd Roman Petrenko (Mon May 04 2009 - 16:18:03 CDT)
- dummy atom mass changed yun luo (Mon May 04 2009 - 14:54:27 CDT)
- Re: dummy atom mass changed Chris Harrison (Mon May 04 2009 - 15:33:57 CDT)
- Re: dummy atom mass changed yun luo (Mon May 04 2009 - 16:24:59 CDT)
- Re: dummy atom mass changed Jerome Henin (Mon May 04 2009 - 17:39:22 CDT)
- Re: dummy atom mass changed daniel aguayo (Mon May 04 2009 - 19:53:14 CDT)
- Re: dummy atom mass changed Chris Harrison (Mon May 04 2009 - 22:24:32 CDT)
- Re: dummy atom mass changed daniel aguayo (Tue May 05 2009 - 10:18:39 CDT)
- Re: dummy atom mass changed Jerome Henin (Tue May 05 2009 - 10:43:48 CDT)
- Re: dummy atom mass changed yun luo (Tue May 05 2009 - 11:49:06 CDT)
- Re: dummy atom mass changed yun luo (Tue May 05 2009 - 12:19:05 CDT)
- Re: dummy atom mass changed Chris Harrison (Tue May 05 2009 - 12:53:00 CDT)
- Re: dummy atom mass changed yun luo (Tue May 05 2009 - 15:26:46 CDT)
- Re: dummy atom mass changed yun luo (Wed May 06 2009 - 11:50:06 CDT)
- Re: dummy atom mass changed Chris Harrison (Wed May 06 2009 - 13:09:26 CDT)
- Re: dummy atom mass changed Floris Buelens (Thu May 07 2009 - 05:09:36 CDT)
- Re: dummy atom mass changed yun luo (Thu May 07 2009 - 11:18:43 CDT)
- Re: dummy atom mass changed yun luo (Tue May 12 2009 - 11:10:11 CDT)
- Re: dummy atom mass changed Jerome Henin (Tue May 12 2009 - 11:51:55 CDT)
- Re: dummy atom mass changed yun luo (Mon May 04 2009 - 16:24:59 CDT)
- Re: dummy atom mass changed Chris Harrison (Mon May 04 2009 - 15:33:57 CDT)
- Regarding amber parameters using NAMD Jorgen Simonsen (Mon May 04 2009 - 03:22:27 CDT)
- NAMD 2.7b1 and clustermatic Gianluca Interlandi (Sun May 03 2009 - 19:26:08 CDT)
- NPAT - NPgT ensemble Bjoern Olausson (Sat May 02 2009 - 07:43:34 CDT)
- CGMD ? Hydrophobic scale BIN ZHANG (Fri May 01 2009 - 17:00:12 CDT)
- Force Fields Goutham (Fri May 01 2009 - 00:36:09 CDT)
- FreeEnergy and minimization Roman Petrenko (Thu Apr 30 2009 - 23:31:55 CDT)
- crash with more than 96 processors (v2.7b1) Grace Brannigan (Thu Apr 30 2009 - 14:49:58 CDT)
- Setting PME Grid DimitryASuplatov (Thu Apr 30 2009 - 11:13:46 CDT)
- two independent groups of constraints Marcin Krol (Thu Apr 30 2009 - 07:44:41 CDT)
- Energy minimization failure DimitryASuplatov (Thu Apr 30 2009 - 05:23:31 CDT)
- running problem ydhuang2727 (Thu Apr 30 2009 - 05:08:22 CDT)
- NAMD 2.7b1 on NCSA Abe Gianluca Interlandi (Wed Apr 29 2009 - 22:16:32 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Peter Freddolino (Thu Apr 30 2009 - 06:41:50 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Gianluca Interlandi (Thu Apr 30 2009 - 12:15:37 CDT)
- topology and parameter files for guanidinium ion Payel Das (Thu Apr 30 2009 - 15:04:48 CDT)
- Re: topology and parameter files for guanidinium ion Peter Freddolino (Thu Apr 30 2009 - 16:32:21 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Peter Freddolino (Thu Apr 30 2009 - 20:11:27 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Gianluca Interlandi (Thu Apr 30 2009 - 22:58:09 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Peter Freddolino (Fri May 01 2009 - 06:41:23 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Gianluca Interlandi (Fri May 01 2009 - 12:18:05 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Gianluca Interlandi (Tue May 05 2009 - 16:53:27 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Gianluca Interlandi (Thu Apr 30 2009 - 12:15:37 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Peter Freddolino (Thu Apr 30 2009 - 06:41:50 CDT)
- Benzene PSF Matt Krems (Wed Apr 29 2009 - 19:04:27 CDT)
- protein shifts out of the water box Eric Userlist (Wed Apr 29 2009 - 18:52:16 CDT)
- FEP tutorial graph question Christopher Hartshorn (Wed Apr 29 2009 - 15:35:27 CDT)
- Re: FEP tutorial graph question Chris Harrison (Wed Apr 29 2009 - 16:17:07 CDT)
- Re: FEP tutorial graph question Jerome Henin (Wed Apr 29 2009 - 18:36:35 CDT)
- cell on namd 2.7b1 alessandro.venturelli_at_univr.it (Wed Apr 29 2009 - 08:10:01 CDT)
- water tail correction Floris Buelens (Wed Apr 29 2009 - 05:51:55 CDT)
- Re: water tail correction Peter Freddolino (Wed Apr 29 2009 - 07:09:45 CDT)
- Re: water tail correction Peter Freddolino (Wed Apr 29 2009 - 10:26:24 CDT)
- Re: water tail correction Floris Buelens (Fri May 22 2009 - 05:40:00 CDT)
- Re: water tail correction Peter Freddolino (Fri May 22 2009 - 13:34:16 CDT)
- Re: water tail correction Floris Buelens (Mon May 25 2009 - 15:51:16 CDT)
- Re: water tail correction Peter Freddolino (Tue May 26 2009 - 14:17:03 CDT)
- Re: water tail correction Floris Buelens (Wed May 27 2009 - 03:16:33 CDT)
- Re: water tail correction Peter Freddolino (Thu May 28 2009 - 13:12:04 CDT)
- Re: water tail correction Peter Freddolino (Fri May 22 2009 - 16:16:59 CDT)
- Re: water tail correction Floris Buelens (Fri May 22 2009 - 05:40:00 CDT)
- how to set initial velocity? uu zhu (Tue Apr 28 2009 - 21:27:37 CDT)
- force-field for ATP Roman Petrenko (Tue Apr 28 2009 - 18:55:05 CDT)
- System expands: CCL4 simulation; NPT(Langevin Piston) satya work (Tue Apr 28 2009 - 16:10:32 CDT)
- crash with more than 96 processors (v2.7b1) Grace Brannigan (Tue Apr 28 2009 - 14:16:07 CDT)
- biotin parameters and topology Brian R Novak (Tue Apr 28 2009 - 12:37:53 CDT)
- +1 offset to VMD index file? DimitryASuplatov (Tue Apr 28 2009 - 08:40:33 CDT)
- Optimizing configuration option for fast calculations DimitryASuplatov (Tue Apr 28 2009 - 07:16:00 CDT)
- Adding a new bond to CHARMM DimitryASuplatov (Sat Apr 25 2009 - 08:23:19 CDT)
- Yet another NAMD speed concerns DimitryASuplatov (Sat Apr 25 2009 - 04:44:44 CDT)
- compile NAMD 2.7b1 on Intel Xeon(R) infiniband cluster 海清 æ¢ (Sat Apr 25 2009 - 01:44:24 CDT)
- Copper parameters for CHARMM DimitryASuplatov (Fri Apr 24 2009 - 11:02:50 CDT)
- how to install NAMD on suse10_ppc64 without xlc bay__gulf618_at_sina.com (Fri Apr 24 2009 - 05:18:04 CDT)
- Namd and MM-PBSA Esteban Gabriel Vega Hissi (Thu Apr 23 2009 - 10:42:49 CDT)
- unsubscribe Matthew Ambrosia (Thu Apr 23 2009 - 09:08:56 CDT)
- Compile Problem xiaojing gong (Thu Apr 23 2009 - 07:42:51 CDT)
- lipidmonolayer balaji nagarajan (Wed Apr 22 2009 - 14:58:25 CDT)
- mapping of force vectors during SMD Jeff Forbes (Wed Apr 22 2009 - 13:42:23 CDT)
- structure problem Ahlam Al-Rawi (Wed Apr 22 2009 - 12:22:29 CDT)
- Constraints in NAMD DimitryASuplatov (Wed Apr 22 2009 - 09:50:37 CDT)
- FATAL ERROR: Periodic cell has become too small for original patch grid! DimitryASuplatov (Wed Apr 22 2009 - 01:44:45 CDT)
- VDW distance in energy minimized conformation Lixia Jin Day (Tue Apr 21 2009 - 17:11:42 CDT)
- can I change coordinate before restart? Mark M Huntress (Tue Apr 21 2009 - 16:03:55 CDT)
- 2.7b1 + CUDA + STMV Charles Taylor (Tue Apr 21 2009 - 09:25:44 CDT)
- tip4p on namd 2.7b fett_at_vtr.net (Tue Apr 21 2009 - 07:45:40 CDT)
- Re: tip4p on namd 2.7b Peter Freddolino (Tue Apr 21 2009 - 09:36:39 CDT)
- Re: tip4p on namd 2.7b Guanglei Cui (Wed Apr 22 2009 - 10:52:19 CDT)
- Re: tip4p on namd 2.7b Peter Freddolino (Wed Apr 22 2009 - 12:19:33 CDT)
- Re: tip4p on namd 2.7b Guanglei Cui (Wed Apr 22 2009 - 16:17:57 CDT)
- PARAM22 and CMAP correction Gianluca Interlandi (Wed Apr 22 2009 - 13:30:48 CDT)
- Re: PARAM22 and CMAP correction Eric H. Lee (Wed Apr 22 2009 - 22:34:19 CDT)
- NAMD 2.7b1 on Abe Gianluca Interlandi (Sat Apr 25 2009 - 12:17:06 CDT)
- soft-core FEP in namd 2.7b Sebastian Stolzenberg (Fri May 08 2009 - 11:57:10 CDT)
- recent papers on MD gotchas with PRNG seeds Brian Bennion (Fri May 08 2009 - 14:20:39 CDT)
- Re: recent papers on MD gotchas with PRNG seeds Peter Freddolino (Sat May 09 2009 - 17:22:43 CDT)
- Re: soft-core FEP in namd 2.7b Chris Harrison (Fri May 08 2009 - 16:14:44 CDT)
- Re: soft-core FEP in namd 2.7b Sebastian Stolzenberg (Sun May 10 2009 - 10:36:47 CDT)
- Re: soft-core FEP in namd 2.7b Jerome Henin (Sun May 10 2009 - 11:50:25 CDT)
- Re: soft-core FEP in namd 2.7b Sebastian Stolzenberg (Sun May 10 2009 - 21:29:32 CDT)
- Re: soft-core FEP in namd 2.7b Jerome Henin (Sun May 10 2009 - 22:19:52 CDT)
- Re: soft-core FEP in namd 2.7b yun luo (Mon May 11 2009 - 12:31:49 CDT)
- Re: soft-core FEP in namd 2.7b Jerome Henin (Mon May 11 2009 - 16:39:37 CDT)
- Re: tip4p on namd 2.7b Guanglei Cui (Wed Apr 22 2009 - 10:52:19 CDT)
- Re: tip4p on namd 2.7b Peter Freddolino (Tue Apr 21 2009 - 09:36:39 CDT)
- Parallel TMD (2.7b) dies : "MPICH internal error" Ali Emileh (Mon Apr 20 2009 - 11:00:11 CDT)
- Re: compiling error of NAMD2.7b1 Joachim Hein (Mon Apr 20 2009 - 06:05:38 CDT)
- Re: compiling error of NAMD2.7b1 BIN ZHANG (Mon Apr 20 2009 - 12:30:17 CDT)
- Re: compiling error of NAMD2.7b1 Peter Freddolino (Mon Apr 20 2009 - 13:12:01 CDT)
- Re: compiling error of NAMD2.7b1 Joachim Hein (Mon Apr 20 2009 - 13:22:11 CDT)
- Re: compiling error of NAMD2.7b1 Peter Freddolino (Mon Apr 20 2009 - 14:49:07 CDT)
- Re: compiling error of NAMD2.7b1 BIN ZHANG (Mon Apr 20 2009 - 13:41:01 CDT)
- Re: compiling error of NAMD2.7b1 Peter Freddolino (Mon Apr 20 2009 - 14:47:09 CDT)
- Re: compiling error of NAMD2.7b1 Joachim Hein (Tue Apr 21 2009 - 04:18:14 CDT)
- Re: compiling error of NAMD2.7b1 Joachim Hein (Mon Apr 20 2009 - 12:53:59 CDT)
- Re: compiling error of NAMD2.7b1 Peter Freddolino (Mon Apr 20 2009 - 13:12:01 CDT)
- Re: compiling error of NAMD2.7b1 BIN ZHANG (Mon Apr 20 2009 - 12:30:17 CDT)
- Peptide in Membrane Environment: loosing water from one leaflet Praveen Agrawal (Mon Apr 20 2009 - 05:53:23 CDT)
- Metadynamics in NAMD ÖÜÎIJý (Mon Apr 20 2009 - 05:50:42 CDT)
- Cylindrical harmonic BC and constraintScaling Elsa Fernanda de Sousa Henriques (Mon Apr 20 2009 - 05:22:25 CDT)
- Pressure coupling and system heating DimitryASuplatov (Mon Apr 20 2009 - 03:38:36 CDT)
- NAMD and new sugar parameter set Gianluca Interlandi (Mon Apr 20 2009 - 00:42:14 CDT)
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- Re: I can't keep my pulling directions the same with the SMD vector Chris Harrison (Sun Apr 19 2009 - 10:25:14 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Mert Gür (Sun Apr 19 2009 - 11:10:11 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Chris Harrison (Sun Apr 19 2009 - 18:27:24 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Mert Gür (Mon Apr 20 2009 - 03:16:39 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Axel Kohlmeyer (Mon Apr 20 2009 - 08:41:22 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Mert Gür (Tue Apr 21 2009 - 02:49:19 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Axel Kohlmeyer (Tue Apr 21 2009 - 07:27:50 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Mert Gür (Sun Apr 19 2009 - 11:10:11 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Chris Harrison (Sun Apr 19 2009 - 10:25:14 CDT)
- compiling error of NAMD2.7b1 zhngbn_at_gmail.com (Sun Apr 19 2009 - 03:02:44 CDT)
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- RE: display all frames simultaneously Luis Gracia (Fri Apr 17 2009 - 00:35:29 CDT)
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- Fwd: psf file creation gurunath katagi (Sun Apr 12 2009 - 19:43:48 CDT)
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- Re: PCA Analysis of CGMD Joshua Adelman (Thu Apr 09 2009 - 10:28:06 CDT)
- RE: PCA Analysis of CGMD Anirban Ghosh (Fri Apr 10 2009 - 04:08:25 CDT)
- RE: PCA Analysis of CGMD Rogan Carr (Fri Apr 10 2009 - 09:47:35 CDT)
- Re: PCA Analysis of CGMD Joshua Adelman (Fri Apr 10 2009 - 10:20:04 CDT)
- Re: PCA Analysis of CGMD Anirban (Wed Apr 15 2009 - 14:44:29 CDT)
- Re: PCA Analysis of CGMD Joshua Adelman (Wed Apr 15 2009 - 09:45:53 CDT)
- Re: PCA Analysis of CGMD Anirban (Wed Apr 15 2009 - 15:42:44 CDT)
- Re: PCA Analysis of CGMD Joshua Adelman (Wed Apr 15 2009 - 10:35:00 CDT)
- Re: PCA Analysis of CGMD Giacomo Fiorin (Wed Apr 15 2009 - 11:20:39 CDT)
- RE: PCA Analysis of CGMD Anirban Ghosh (Fri Apr 10 2009 - 04:08:25 CDT)
- Re: PCA Analysis of CGMD Joshua Adelman (Thu Apr 09 2009 - 10:28:06 CDT)
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- Evaluating kinetic energy from a modified DCD file Mert Gür (Wed Apr 08 2009 - 14:33:05 CDT)
- Re: Evaluating kinetic energy from a modified DCD file Peter Freddolino (Wed Apr 08 2009 - 15:15:00 CDT)
- Re: Evaluating kinetic energy from a modified DCD file Mert Gür (Wed Apr 08 2009 - 16:57:01 CDT)
- Re: Evaluating kinetic energy from a modified DCD file JT (Fri Apr 10 2009 - 11:36:52 CDT)
- Re: Evaluating kinetic energy from a modified DCD file Mert Gür (Fri Apr 10 2009 - 12:52:08 CDT)
- RE: Evaluating kinetic energy from a modified DCD file Tibbitt, Jeffrey A. (Fri Apr 10 2009 - 15:03:24 CDT)
- RE: Evaluating kinetic energy from a modified DCD file JT (Sat Apr 11 2009 - 03:47:57 CDT)
- Re: Evaluating kinetic energy from a modified DCD file Mert Gür (Sun Apr 12 2009 - 08:11:21 CDT)
- Re: Evaluating kinetic energy from a modified DCD file Peter Freddolino (Wed Apr 08 2009 - 15:15:00 CDT)
- problem namd2-MPICH jose correa (Wed Apr 08 2009 - 14:05:09 CDT)
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- constraints dota (Wed Apr 08 2009 - 04:23:40 CDT)
- Writing 3 subsequent timesteps to the DCD file Mert Gür (Tue Apr 07 2009 - 06:24:18 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Axel Kohlmeyer (Tue Apr 07 2009 - 07:45:54 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Mert Gür (Wed Apr 08 2009 - 04:44:09 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Axel Kohlmeyer (Wed Apr 08 2009 - 08:23:26 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file David Hardy (Wed Apr 08 2009 - 09:33:40 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Axel Kohlmeyer (Wed Apr 08 2009 - 10:26:17 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Mert Gür (Wed Apr 08 2009 - 13:40:43 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Mert Gür (Wed Apr 08 2009 - 14:36:45 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Grace Brannigan (Wed Apr 08 2009 - 17:36:19 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Mert Gür (Fri Apr 10 2009 - 10:24:23 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Axel Kohlmeyer (Fri Apr 10 2009 - 12:02:06 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Giacomo Fiorin (Wed Apr 08 2009 - 10:22:46 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Axel Kohlmeyer (Wed Apr 08 2009 - 08:23:26 CDT)
- outputname and restartname Neelanjana Sengupta (Tue Apr 07 2009 - 01:45:19 CDT)
- NAMD job dies on 2-quad core server vivek.viv.sharma_at_gmail.com (Sun Apr 05 2009 - 23:45:28 CDT)
- Re: NAMD job dies on 2-quad core server Axel Kohlmeyer (Mon Apr 06 2009 - 08:44:54 CDT)
- Re: Re: NAMD job dies on 2-quad core server vivek.viv.sharma_at_gmail.com (Thu Apr 09 2009 - 01:44:01 CDT)
- Re: Re: NAMD job dies on 2-quad core server Axel Kohlmeyer (Thu Apr 09 2009 - 09:03:24 CDT)
- Re: NAMD job dies on 2-quad core server Gengbin Zheng (Thu Apr 09 2009 - 10:22:04 CDT)
- Re: Re: NAMD job dies on 2-quad core server vivek.viv.sharma_at_gmail.com (Thu Apr 09 2009 - 22:32:12 CDT)
- Re: NAMD job dies on 2-quad core server Gengbin Zheng (Thu Apr 09 2009 - 23:14:31 CDT)
- Re: Re: NAMD job dies on 2-quad core server vivek.viv.sharma_at_gmail.com (Thu Apr 09 2009 - 01:44:01 CDT)
- Re: NAMD job dies on 2-quad core server Axel Kohlmeyer (Mon Apr 06 2009 - 08:44:54 CDT)
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- how to config two different files for fixed atoms karthik s (Tue Mar 31 2009 - 06:54:10 CDT)
- smd direction Wang,Ying (Mon Mar 30 2009 - 10:04:28 CDT)
- NAMD 2.7b1 on Teragrid Ali Emileh (Mon Mar 30 2009 - 09:55:33 CDT)
- Pulling atoms in different directions Rahul Bhowmik (Sun Mar 29 2009 - 15:59:01 CDT)
- Error generating file.psf for cholesterol, missing coordinates in file.pdb. Leonardo Herrera (Sun Mar 29 2009 - 14:56:20 CDT)
- NAMD is too slow?! DimitryASuplatov (Sun Mar 29 2009 - 04:37:39 CDT)
- Interactive protonation DimitryASuplatov (Sat Mar 28 2009 - 16:46:51 CDT)
- NAMD and CFF forcefields C. Denise Enekwa (Sat Mar 28 2009 - 13:22:36 CDT)
- modifying a nucleobase jfgaff_at_ncsu.edu (Sat Mar 28 2009 - 09:05:01 CDT)
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- Re: use of tiElecLambdaStart (NAMD 2.7b1) Chris Harrison (Fri Mar 27 2009 - 14:33:04 CDT)
- Re: use of tiElecLambdaStart (NAMD 2.7b1) Chris Harrison (Fri Mar 27 2009 - 15:45:41 CDT)
- Re: use of tiElecLambdaStart (NAMD 2.7b1) Jerome Henin (Fri Mar 27 2009 - 16:32:31 CDT)
- Re: use of tiElecLambdaStart (NAMD 2.7b1) brmorgan_at_clarku.edu (Mon Mar 30 2009 - 13:21:34 CDT)
- Re: use of tiElecLambdaStart (NAMD 2.7b1) Floris Buelens (Tue Mar 31 2009 - 04:29:56 CDT)
- Re: use of tiElecLambdaStart (NAMD 2.7b1) Chris Harrison (Fri Mar 27 2009 - 14:33:04 CDT)
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- NAMD 2.7b1 release Jim Phillips (Wed Mar 25 2009 - 10:16:18 CDT)
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- About CUDA version of NAMD 2.7 B1 wang (Wed Mar 25 2009 - 00:57:33 CDT)
- Gromacs simulation not running in NAMD abhijit ramachandran (Mon Mar 23 2009 - 21:19:32 CDT)
- alanine dipeptide: no dihdral energy terms? Sebastian Stolzenberg (Mon Mar 23 2009 - 22:33:03 CDT)
- Re: alanine dipeptide: no dihdral energy terms? Peter Freddolino (Mon Mar 23 2009 - 22:45:01 CDT)
- Re: alanine dipeptide: no dihdral energy terms? Sebastian Stolzenberg (Thu Mar 26 2009 - 19:21:04 CDT)
- Re: alanine dipeptide: no dihdral energy terms? Peter Freddolino (Fri Mar 27 2009 - 14:42:54 CDT)
- how to do: FEP e2?, a protonating mutation? Sebastian Stolzenberg (Tue Apr 07 2009 - 19:15:19 CDT)
- Re: how to do: FEP e2?, a protonating mutation? Sébastien Légaré (Thu Apr 09 2009 - 10:48:06 CDT)
- Unfavorable anti conformation after GLUP patching? Sebastian Stolzenberg (Tue Apr 14 2009 - 19:13:21 CDT)
- Re: Unfavorable anti conformation after GLUP patching? Sébastien Légaré (Wed Apr 15 2009 - 22:06:14 CDT)
- Re: Unfavorable anti conformation after GLUP patching? Sebastian Stolzenberg (Thu Apr 16 2009 - 11:00:17 CDT)
- Re: Re: Unfavorable anti conformation after GLUP patching? Sébastien Légaré (Sat Apr 18 2009 - 21:43:22 CDT)
- Re: how to do: FEP e2?, a protonating mutation? Sébastien Légaré (Wed Apr 15 2009 - 22:32:27 CDT)
- Re: alanine dipeptide: no dihdral energy terms? Peter Freddolino (Mon Mar 23 2009 - 22:45:01 CDT)
- Re: Gromacs simulation not running in NAMD Peter Freddolino (Mon Mar 23 2009 - 22:43:27 CDT)
- alanine dipeptide: no dihdral energy terms? Sebastian Stolzenberg (Mon Mar 23 2009 - 22:33:03 CDT)
- polymer topology file accomp lin (Mon Mar 23 2009 - 07:41:38 CDT)
- Re: vmd-l: GTP topology file Peter Freddolino (Fri Mar 20 2009 - 12:03:01 CDT)
- GTP topology file tiziano gallo cassarino (Fri Mar 20 2009 - 08:47:23 CDT)
- acridine orange Rudra Banerjee (Thu Mar 19 2009 - 23:54:50 CDT)
- Re: FW: NAMD 2.6, AMD64, MVAPICH2 compile error Thomas C. Bishop (Thu Mar 19 2009 - 16:31:27 CDT)
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- Re: Selectively turning off electrostatic interactions JC Gumbart (Wed Mar 11 2009 - 12:07:03 CDT)
- Re: Selectively turning off electrostatic interactions Chris Harrison (Wed Mar 11 2009 - 15:28:46 CDT)
- Re: some problem about ABF Jerome Henin (Wed Mar 11 2009 - 09:18:14 CDT)
- FW: Water density of water Box Shahid Qamar (Wed Mar 11 2009 - 07:07:15 CDT)
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- Problem to generate water segments and lipid reading in membrane Leonardo Herrera (Tue Mar 10 2009 - 05:17:36 CDT)
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- about calculation of PMF from SMD trajectories Falgun Shah (Wed Mar 04 2009 - 11:58:52 CST)
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- help running NAMD energy at multiple stable temperatures (newbie) Marie N (Mon Mar 02 2009 - 23:32:04 CST)
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- Minimization convergence issue Brittany Morgan (Mon Mar 02 2009 - 09:59:21 CST)
- Re: Minimization convergence issue Peter Freddolino (Mon Mar 02 2009 - 10:29:32 CST)
- RE: Minimization convergence issue Brittany Morgan (Mon Mar 02 2009 - 10:53:55 CST)
- RE: Minimization convergence issue Brittany Morgan (Wed Mar 04 2009 - 13:36:38 CST)
- Re: Minimization convergence issue Chris Harrison (Wed Mar 04 2009 - 19:41:06 CST)
- RE: Minimization convergence issue Brittany Morgan (Thu Mar 05 2009 - 07:56:47 CST)
- Re: Minimization convergence issue Chris Harrison (Thu Mar 05 2009 - 17:05:51 CST)
- Re: Minimization convergence issue Christopher Gillespie (Thu Mar 05 2009 - 12:04:02 CST)
- RE: Minimization convergence issue Brittany Morgan (Thu Mar 05 2009 - 12:46:28 CST)
- RE: Minimization convergence issue Brittany Morgan (Mon Mar 02 2009 - 10:53:55 CST)
- Re: Minimization convergence issue Peter Freddolino (Mon Mar 02 2009 - 10:29:32 CST)
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- Re: Background load problem Peter Freddolino (Thu Feb 26 2009 - 07:50:36 CST)
- Re: Background load problem Anirban (Thu Feb 26 2009 - 08:15:04 CST)
- Re: Background load problem Nicholas M Glykos (Thu Feb 26 2009 - 09:29:58 CST)
- Re: Background load problem Axel Kohlmeyer (Thu Feb 26 2009 - 10:13:06 CST)
- Re: Background load problem Peter Freddolino (Thu Feb 26 2009 - 11:45:00 CST)
- Re: Background load problem Anirban (Fri Feb 27 2009 - 03:38:16 CST)
- Re: Background load problem Peter Freddolino (Fri Feb 27 2009 - 15:10:29 CST)
- Re: Background load problem Anirban (Thu Feb 26 2009 - 08:15:04 CST)
- Re: Background load problem Peter Freddolino (Thu Feb 26 2009 - 07:50:36 CST)
- loading of large dcd files sripad chandan (Wed Feb 25 2009 - 23:54:58 CST)
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- Re: vmd-l: Membrane builder ?'s Christopher Hartshorn (Tue Feb 24 2009 - 00:47:57 CST)
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- A beginner's question for using NAMD to do cell membrane simulation and molecular transportation Xu Dong (Sat Feb 21 2009 - 14:23:49 CST)
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- Re: Constant pressure simulation: can I get the changed volume? Fred (Rui FENG) (Thu Feb 19 2009 - 04:26:50 CST)
- Constant pressure simulation: can I get the changed volume? Fred (Rui FENG) (Thu Feb 19 2009 - 01:52:55 CST)
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- Autopsf error with a modified top file CHINDEA Vlad (Wed Feb 18 2009 - 15:17:52 CST)
- Re: Autopsf error with a modified top file Peter Freddolino (Wed Feb 18 2009 - 15:24:59 CST)
- RE: Autopsf error with a modified top file CHINDEA Vlad (Thu Feb 19 2009 - 18:15:45 CST)
- Re: Autopsf error with a modified top file Peter Freddolino (Thu Feb 19 2009 - 19:52:52 CST)
- RE: Autopsf error with a modified top file CHINDEA Vlad (Fri Feb 20 2009 - 19:28:28 CST)
- Re: Autopsf error with a modified top file Peter Freddolino (Fri Feb 20 2009 - 23:19:22 CST)
- RE: Autopsf error with a modified top file CHINDEA Vlad (Sat Feb 21 2009 - 06:04:19 CST)
- RE: Autopsf error with a modified top file CHINDEA Vlad (Thu Feb 19 2009 - 18:15:45 CST)
- Re: Autopsf error with a modified top file Peter Freddolino (Wed Feb 18 2009 - 15:24:59 CST)
- fail to run replica exchange on more than one node Linchen Gong (Wed Feb 18 2009 - 01:31:24 CST)
- Thiol on gold simulation in NAMD S.K. Ghosh (Tue Feb 17 2009 - 14:14:36 CST)
- Re: Thiol on gold simulation in NAMD Axel Kohlmeyer (Tue Feb 17 2009 - 14:54:51 CST)
- how can i get the energy of a molecule of a whole system? Wang,Ying (Tue Feb 17 2009 - 10:30:11 CST)
- Problem running NAMD on ranger@TACC shayan_at_msu.edu (Tue Feb 17 2009 - 07:01:27 CST)
- Forces on Atoms and Potential Energy Mohamed Seyam (Mon Feb 16 2009 - 13:57:01 CST)
- unsubscribe Vinit Rege (Mon Feb 16 2009 - 12:07:11 CST)
- log file from 3 different protein simulations sripad chandan (Mon Feb 16 2009 - 05:50:36 CST)
- Re: FEP/binding free energy difference WT vs Mut Chris Harrison (Fri Feb 13 2009 - 17:57:21 CST)
- FEP/binding free energy difference WT vs Mut Luis Cunha (Fri Feb 13 2009 - 16:43:27 CST)
- Membrane Proteins Tutorial Marcos Sotomayor (Fri Feb 13 2009 - 16:25:15 CST)
- unsubscribe Lee, Se I (Thu Feb 12 2009 - 13:26:01 CST)
- ligand flies away from binding pocket Osman Yogurtcu (Thu Feb 12 2009 - 11:39:04 CST)
- namd ubuntu-instalation jose correa (Thu Feb 12 2009 - 09:23:15 CST)
- (no subject) gurunath katagi (Thu Feb 12 2009 - 03:13:47 CST)
- namd cvs compilation with a maximum number of cores to run on Vlad Cojocaru (Thu Feb 12 2009 - 03:11:50 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Peter Freddolino (Thu Feb 12 2009 - 08:32:59 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Vlad Cojocaru (Thu Feb 12 2009 - 09:04:14 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Peter Freddolino (Thu Feb 12 2009 - 09:41:27 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Axel Kohlmeyer (Thu Feb 12 2009 - 10:35:05 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Andrew Emerson (Fri Feb 13 2009 - 03:36:30 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Axel Kohlmeyer (Fri Feb 13 2009 - 07:21:33 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Vlad Cojocaru (Thu Feb 12 2009 - 09:04:14 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Peter Freddolino (Thu Feb 12 2009 - 08:32:59 CST)
- reg dynamics hari prasad (Thu Feb 12 2009 - 01:58:55 CST)
- (Á¦¸ñ ¾øÀ½) Taeho Kim (Wed Feb 11 2009 - 22:29:19 CST)
- pressure profile calculations Grace Brannigan (Wed Feb 11 2009 - 16:58:06 CST)
- cuda 1.0 binaries on cuda 1.1 Roman Petrenko (Wed Feb 11 2009 - 13:47:32 CST)
- Need Charmm FF for Gangliosides bo liu (Wed Feb 11 2009 - 11:36:19 CST)
- (no subject) gurunath katagi (Wed Feb 11 2009 - 10:49:16 CST)
- center of mass for SMD Falgun Shah (Tue Feb 10 2009 - 17:52:06 CST)
- How to specify processors for running VMD on a cluster? Yinglong Miao (Tue Feb 10 2009 - 10:45:27 CST)
- tmd algorithm Elif Ozkirimli (Tue Feb 10 2009 - 09:22:58 CST)
- Periodic boundary condition in a membrane simulation Eric Hu (Mon Feb 09 2009 - 17:28:38 CST)
- any experiences with executing parallel NAMD in a NAMD simulation Yinglong Miao (Mon Feb 09 2009 - 15:59:07 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Peter Freddolino (Mon Feb 09 2009 - 16:26:39 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Yinglong Miao (Mon Feb 09 2009 - 19:56:44 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Peter Freddolino (Mon Feb 09 2009 - 22:13:43 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Yinglong Miao (Mon Feb 09 2009 - 22:26:37 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Peter Freddolino (Tue Feb 10 2009 - 09:26:02 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Yinglong Miao (Tue Feb 10 2009 - 10:13:56 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Peter Freddolino (Tue Feb 10 2009 - 12:45:34 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Yinglong Miao (Mon Feb 09 2009 - 19:56:44 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Peter Freddolino (Mon Feb 09 2009 - 16:26:39 CST)
- Take a look at jaxtr! Sudipta Sinha (Sun Feb 08 2009 - 22:20:40 CST)
- Accessing atoms and velocities during NVE run Nd S (Fri Feb 06 2009 - 10:57:02 CST)
- eucb - beta testers wanted for trajectory analysis program Athanassios Stavrakoudis (Thu Feb 05 2009 - 18:18:08 CST)
- "Hands-On" Workshop on Computational Biophysics, July 6-10 and August 10-14, 2009 TCBG Workshop (Thu Feb 05 2009 - 15:52:30 CST)
- Fwd:Re: TCL: divide by zero supram_at_nankai.edu.cn (Thu Feb 05 2009 - 10:28:45 CST)
- TCL: divide by zero supram_at_nankai.edu.cn (Thu Feb 05 2009 - 10:08:11 CST)
- TCL: divide by zero supram_at_nankai.edu.cn (Thu Feb 05 2009 - 06:26:11 CST)
- Fwd:Re: ABF-Zcoord: ÁõÓý (Wed Feb 04 2009 - 22:04:40 CST)
- Fatal error in configuration file Corey Fugate (Wed Feb 04 2009 - 21:05:36 CST)
- ABF:restraint in free energy calculation in Zcoord-method ÁõÓý (Tue Feb 03 2009 - 22:15:42 CST)
- Variable results for the same simulation Nd S (Tue Feb 03 2009 - 12:18:24 CST)
- ABF-Zcoord: ÁõÓý (Tue Feb 03 2009 - 07:29:23 CST)
- tcl script fett_at_vtr.net (Mon Feb 02 2009 - 21:31:04 CST)
- generating xsc and vel files David A. Horita (Mon Feb 02 2009 - 10:29:29 CST)
- Correlation matrix of the Ca atoms sripad chandan (Sun Feb 01 2009 - 22:46:14 CST)
- Re: Correlation matrix of the Ca atoms Joshua Adelman (Sun Feb 01 2009 - 23:22:07 CST)
- Re: Correlation matrix of the Ca atoms Nicholas M Glykos (Mon Feb 02 2009 - 02:17:39 CST)
- FEP with fixed explicit environment? Sebastian Stolzenberg (Thu Mar 12 2009 - 18:50:32 CDT)
- Re: FEP with fixed explicit environment? Chris Harrison (Thu Mar 12 2009 - 22:05:24 CDT)
- Re: FEP with fixed explicit environment? Sebastian Stolzenberg (Fri Mar 13 2009 - 10:58:32 CDT)
- Re: FEP with fixed explicit environment? Sebastian Stolzenberg (Fri Mar 13 2009 - 16:42:35 CDT)
- FEP with fixed explicit environment? Sebastian Stolzenberg (Sun Mar 15 2009 - 12:03:28 CDT)
- Re: FEP with fixed explicit environment? Sebastian Stolzenberg (Tue Mar 17 2009 - 13:21:12 CDT)
- Re: FEP with fixed explicit environment? Peter Freddolino (Tue Mar 17 2009 - 14:10:07 CDT)
- multiple FEP experiments in one NAMD-FEP run? Sebastian Stolzenberg (Tue Mar 17 2009 - 15:51:14 CDT)
- Re: multiple FEP experiments in one NAMD-FEP run? Peter Freddolino (Wed Mar 18 2009 - 15:42:27 CDT)
- tclforces included in the NAMD-FEP \delta_G values? Sebastian Stolzenberg (Thu Mar 19 2009 - 13:11:10 CDT)
- Re: tclforces included in the NAMD-FEP \delta_G values? Jerome Henin (Thu Mar 19 2009 - 15:47:32 CDT)
- alchemify with CMAP? Sebastian Stolzenberg (Thu Apr 16 2009 - 19:11:53 CDT)
- Re: alchemify with CMAP? Chris Chipot (Thu Apr 16 2009 - 19:21:19 CDT)
- Re: alchemify with CMAP? Jerome Henin (Thu Apr 16 2009 - 19:21:51 CDT)
- Re: Re: alchemify with CMAP? Sébastien Légaré (Fri Apr 17 2009 - 11:01:08 CDT)
- Re: Re: alchemify with CMAP? Jerome Henin (Fri Apr 17 2009 - 14:44:11 CDT)
- Re: Re: alchemify with CMAP? Jerome Henin (Mon Apr 20 2009 - 11:42:05 CDT)
- FEP with fixed explicit environment? Sebastian Stolzenberg (Thu Mar 12 2009 - 18:51:05 CDT)
- FEP with fixed explicit environment? Sebastian Stolzenberg (Thu Mar 12 2009 - 18:50:32 CDT)
- combining abf reaction path Arturas Ziemys (Sat Jan 31 2009 - 12:20:55 CST)
- pdb and rmsd Falgun Shah (Fri Jan 30 2009 - 13:46:42 CST)
- Aligning the distance between two centroids with an axis Mert Gür (Fri Jan 30 2009 - 04:02:55 CST)
- Re: Aligning the distance between two centroids with an axis Nicholas M Glykos (Fri Jan 30 2009 - 05:08:19 CST)
- Re: Aligning the distance between two centroids with an axis Grace Brannigan (Fri Jan 30 2009 - 10:01:55 CST)
- Re: Aligning the distance between two centroids with an axis Chris Harrison (Fri Jan 30 2009 - 21:31:43 CST)
- FEP on NAMD2.6 versus latest CVS NAMD build Christopher Hartshorn (Fri Jan 30 2009 - 00:54:54 CST)
- running NAMD on Kraken Cray-XT4 Xu, Jiancong (Thu Jan 29 2009 - 15:44:58 CST)
- New open() for DCDs in v.2.6 ? Nicholas M Glykos (Thu Jan 29 2009 - 11:34:37 CST)
- loading large dcd files sripad chandan (Thu Jan 29 2009 - 04:30:29 CST)
- asymmetric water found! OZGE ENGIN (Wed Jan 28 2009 - 07:26:07 CST)
- value 9999999.99999 during simulation uma mageshwari (Wed Jan 28 2009 - 04:11:57 CST)
- alpha character error in the psf file OZGE ENGIN (Wed Jan 28 2009 - 03:30:26 CST)
- (no subject) OZGE ENGIN (Wed Jan 28 2009 - 03:29:03 CST)
- how to add ions to a system uma mageshwari (Wed Jan 28 2009 - 03:18:19 CST)
- how to add ions to a system uma mageshwari (Wed Jan 28 2009 - 01:57:09 CST)
- how to add ions to a system uma mageshwari (Wed Jan 28 2009 - 01:08:12 CST)
- Rosetta Academic Training Workshop Nir London (Tue Jan 27 2009 - 07:04:42 CST)
- NAMD on a virtual grid Benjamin Bouvier (Mon Jan 26 2009 - 09:38:30 CST)
- RMSD and merging trajectories Falgun Shah (Sat Jan 24 2009 - 17:20:27 CST)
- Stratification schemes Chris Chipot (Sat Jan 24 2009 - 16:28:37 CST)
- NADP jose correa (Fri Jan 23 2009 - 18:43:07 CST)
- Re: some recommendations for parametrizing new molecules requiredþ CHINDEA Vlad (Fri Jan 23 2009 - 16:30:16 CST)
- Re: problems-protein minimization jose correa (Fri Jan 23 2009 - 14:27:59 CST)
- problems-protein minimization jose correa (Fri Jan 23 2009 - 12:40:22 CST)
- some recommendations for parametrizing new molecules required CHINDEA Vlad (Fri Jan 23 2009 - 03:31:04 CST)
- Re: some recommendations for parametrizing new molecules required Christopher Gillespie (Fri Jan 23 2009 - 07:36:30 CST)
- Re: some recommendations for parametrizing new molecules required Axel Kohlmeyer (Fri Jan 23 2009 - 09:20:50 CST)
- Re: some recommendations for parametrizing new molecules required JC Gumbart (Fri Jan 23 2009 - 11:17:09 CST)
- use of berendsenPressure during heating Falgun Shah (Thu Jan 22 2009 - 22:22:29 CST)
- abf convergence problems Jorgen Simonsen (Thu Jan 22 2009 - 11:16:36 CST)
- I: Running Charm++ over MPI does not work andy.mastellone_at_alice.it (Thu Jan 22 2009 - 08:23:58 CST)
- Running Charm++ over MPI does not work andy.mastellone_at_alice.it (Thu Jan 22 2009 - 07:20:28 CST)
- Hexafluoro-2-propanol (HFIP) force parameters Dong Luo (Wed Jan 21 2009 - 15:04:43 CST)
- Re: CUDA version status Dow_Hurst (Wed Jan 21 2009 - 13:12:32 CST)
- IBVerbs NAMD build segfaults Jason Russler (Wed Jan 21 2009 - 08:47:28 CST)
- double-wide sampling with soft-core Sébastien Légaré (Tue Jan 20 2009 - 14:27:32 CST)
- Re: double-wide sampling with soft-core Jerome Henin (Wed Jan 21 2009 - 16:02:24 CST)
- Re: double-wide sampling with soft-core Chris Chipot (Wed Jan 21 2009 - 17:32:52 CST)
- Re: double-wide sampling with soft-core Floris Buelens (Thu Jan 22 2009 - 04:58:40 CST)
- Re: double-wide sampling with soft-core Chris Harrison (Thu Jan 22 2009 - 11:21:15 CST)
- Re: double-wide sampling with soft-core Peter Freddolino (Thu Jan 22 2009 - 11:34:07 CST)
- Re: double-wide sampling with soft-core Floris Buelens (Thu Jan 22 2009 - 12:02:36 CST)
- Re: double-wide sampling with soft-core Chris Chipot (Thu Jan 22 2009 - 12:23:55 CST)
- Re: double-wide sampling with soft-core Floris Buelens (Thu Jan 22 2009 - 13:25:19 CST)
- Re: double-wide sampling with soft-core Jerome Henin (Thu Jan 22 2009 - 11:35:39 CST)
- Re: double-wide sampling with soft-core Chris Harrison (Thu Jan 22 2009 - 11:48:23 CST)
- Re: double-wide sampling with soft-core Jerome Henin (Wed Jan 21 2009 - 16:02:24 CST)
- CUDA version status Dow Hurst (Tue Jan 20 2009 - 12:39:20 CST)
- (no subject) gurunath katagi (Tue Jan 20 2009 - 08:25:06 CST)
- Single vs. Double precision Neelanjana Sengupta (Mon Jan 19 2009 - 05:27:27 CST)
- The limit of atom number on Blue Gene/L Fred (Rui FENG) (Mon Jan 19 2009 - 02:09:15 CST)
- TMD comments Michael Feig (Fri Jan 16 2009 - 23:06:07 CST)
- syntax error in expression "(": premature end of expression - namdstats CHINDEA Vlad (Fri Jan 16 2009 - 17:08:54 CST)
- Problems deciphering fepout Christopher Hartshorn (Fri Jan 16 2009 - 16:28:21 CST)
- SMD output dimka (Fri Jan 16 2009 - 12:59:43 CST)
- SMD output Dmitry Lupyan (Thu Jan 15 2009 - 16:50:08 CST)
- ABF calculation with TclForces script in the configuration file govardhan reddy (Fri Jan 16 2009 - 09:18:40 CST)
- advice on van Hove Arturas Ziemys (Thu Jan 15 2009 - 12:08:40 CST)
- Energy drif in NVE ensemble eprates_at_iqm.unicamp.br (Thu Jan 15 2009 - 11:51:54 CST)
- dielectric parameter? BIN ZHANG (Thu Jan 15 2009 - 01:10:36 CST)
- problem in fitting Maxwell-Boltzmann distribution CHINDEA Vlad (Wed Jan 14 2009 - 17:08:48 CST)
- Re: problem in fitting Maxwell-Boltzmann distribution JC Gumbart (Wed Jan 14 2009 - 19:00:12 CST)
- RE: problem in fitting Maxwell-Boltzmann distribution CHINDEA Vlad (Thu Jan 15 2009 - 06:39:47 CST)
- Re: problem in fitting Maxwell-Boltzmann distribution Peter Freddolino (Thu Jan 15 2009 - 08:22:19 CST)
- RE: problem in fitting Maxwell-Boltzmann distribution CHINDEA Vlad (Fri Jan 16 2009 - 13:30:26 CST)
- Re: problem in fitting Maxwell-Boltzmann distribution Peter Freddolino (Fri Jan 16 2009 - 13:48:27 CST)
- RE: problem in fitting Maxwell-Boltzmann distribution CHINDEA Vlad (Thu Jan 15 2009 - 06:39:47 CST)
- Re: problem in fitting Maxwell-Boltzmann distribution JC Gumbart (Wed Jan 14 2009 - 19:00:12 CST)
- error during heating of the minimized system: (please reply!) Falgun Shah (Wed Jan 14 2009 - 01:08:28 CST)
- question about cellBasisVector*? BIN ZHANG (Tue Jan 13 2009 - 00:13:25 CST)
- Creating bonds during a run Marcin S. (Mon Jan 12 2009 - 09:41:23 CST)
- Question on mutator in VMD Jianping Lin (Sun Jan 11 2009 - 17:00:54 CST)
- binary trajectories karthik s (Fri Jan 09 2009 - 04:53:54 CST)
- NAMD disk writes and quota overflow Jeff Forbes (Thu Jan 08 2009 - 15:45:05 CST)
- how to save output file in plain text? Segun Jung (Thu Jan 08 2009 - 15:09:02 CST)
- Single or double precision? mm148881 (Thu Jan 08 2009 - 13:09:21 CST)
- Inorganic compounds Casey,Richard (Thu Jan 08 2009 - 12:20:34 CST)
- FATAL ERROR: Setting parameter constraints from script failed! Do Nhu Trang (Thu Jan 08 2009 - 09:57:28 CST)
- Re: FATAL ERROR: Setting parameter constraints from script failed! Axel Kohlmeyer (Thu Jan 08 2009 - 10:58:05 CST)
- Re: FATAL ERROR: Setting parameter constraints from script failed! Joshua Adelman (Thu Jan 08 2009 - 11:14:24 CST)
- Re: FATAL ERROR: Setting parameter constraints from script failed! Do Nhu Trang (Fri Jan 09 2009 - 08:31:02 CST)
- Re: FATAL ERROR: Setting parameter constraints from script failed! Axel Kohlmeyer (Fri Jan 09 2009 - 08:54:26 CST)
- Re: FATAL ERROR: Setting parameter constraints from script failed! Do Nhu Trang (Fri Jan 09 2009 - 10:17:02 CST)
- Re: FATAL ERROR: Setting parameter constraints from script failed! Joshua Adelman (Thu Jan 08 2009 - 11:14:24 CST)
- Re: FATAL ERROR: Setting parameter constraints from script failed! Axel Kohlmeyer (Thu Jan 08 2009 - 10:58:05 CST)
- tcl forces interface Vlad Cojocaru (Wed Jan 07 2009 - 04:36:13 CST)
- Gradient tolerance nan for A three-atom simulation accomp lin (Mon Jan 05 2009 - 23:09:41 CST)
- RE: Gradient tolerance nan for A three-atom simulation JC Gumbart (Mon Jan 05 2009 - 23:24:35 CST)
- RE: Gradient tolerance nan for A three-atom simulation accomp lin (Tue Jan 06 2009 - 22:20:18 CST)
- Re: Gradient tolerance nan for A three-atom simulation Peter Freddolino (Thu Jan 08 2009 - 13:19:39 CST)
- Re: Gradient tolerance nan for A three-atom simulation accomp lin (Fri Jan 09 2009 - 02:51:43 CST)
- Re: Gradient tolerance nan for A three-atom simulation Peter Freddolino (Fri Jan 09 2009 - 16:14:33 CST)
- Re: Gradient tolerance nan for A three-atom simulation Peter Freddolino (Fri Jan 09 2009 - 16:14:48 CST)
- Re: Gradient tolerance nan for A three-atom simulation BIN ZHANG (Mon Jan 12 2009 - 12:03:52 CST)
- Re: Gradient tolerance nan for A three-atom simulation Peter Freddolino (Mon Jan 12 2009 - 12:17:49 CST)
- RE: Gradient tolerance nan for A three-atom simulation accomp lin (Tue Jan 06 2009 - 22:20:18 CST)
- RE: Gradient tolerance nan for A three-atom simulation JC Gumbart (Mon Jan 05 2009 - 23:24:35 CST)
- Re: namdcvs Achani.K.Yatawara_at_Dartmouth.edu (Mon Jan 05 2009 - 13:32:34 CST)
- Re: Re: namdcvs Peter Freddolino (Mon Jan 05 2009 - 13:51:02 CST)
- Re: Re: namdcvs Peter Freddolino (Mon Jan 05 2009 - 14:02:58 CST)
- Re: Re: namdcvs BIN ZHANG (Mon Jan 05 2009 - 14:12:59 CST)
- Problem with number of steps > 1000000 Anirban Ghosh (Mon Jan 05 2009 - 07:52:55 CST)
- Confira meu perfil no Facebook Ariovaldo De Souza Junior (Sat Jan 03 2009 - 12:31:41 CST)
- How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely sunita gupta (Fri Jan 02 2009 - 03:58:37 CST)
- Re: namdcvs Re: how to apply restraints for phi and psi for alpha helix regions Leonardo Trabuco (Fri Jan 02 2009 - 02:55:40 CST)
- How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely. sunita gupta (Wed Dec 31 2008 - 00:27:08 CST)
- base stacking analysis of the trajectory of a nucleic acids simulation Tianjiao Wang (Tue Dec 30 2008 - 15:54:31 CST)
- gpu pressure control Daniel Miscevski (Sun Dec 28 2008 - 23:10:46 CST)
- compiling NAMD failed on windows with Cygwin accomp lin (Sun Dec 28 2008 - 22:32:51 CST)
- Re: compiling NAMD failed on windows with Cygwin Axel Kohlmeyer (Mon Dec 29 2008 - 09:36:45 CST)
- Re: compiling NAMD failed on windows with Cygwin accomp lin (Fri Jan 09 2009 - 22:06:37 CST)
- Re: compiling NAMD failed on windows with Cygwin Axel Kohlmeyer (Sat Jan 10 2009 - 09:20:44 CST)
- Re: compiling NAMD failed on windows with Cygwin accomp lin (Sun Jan 11 2009 - 02:02:54 CST)
- Re: compiling NAMD failed on windows with Cygwin Axel Kohlmeyer (Sun Jan 11 2009 - 14:11:04 CST)
- Re: compiling NAMD failed on windows with Cygwin accomp lin (Tue Jan 13 2009 - 22:31:12 CST)
- Re: compiling NAMD failed on windows with Cygwin accomp lin (Fri Jan 09 2009 - 22:06:37 CST)
- Re: compiling NAMD failed on windows with Cygwin Axel Kohlmeyer (Mon Dec 29 2008 - 09:36:45 CST)
- compiling charm++ failed on window with Cygwin accomp lin (Sun Dec 28 2008 - 01:23:13 CST)
- Changing the Secondary Structure of a Protein MIke S (Sun Dec 28 2008 - 01:18:23 CST)
- NAMD-L: autoionize error jfgaff_at_ncsu.edu (Fri Dec 26 2008 - 13:21:17 CST)
- solvating protein Jorgen Simonsen (Fri Dec 26 2008 - 10:27:31 CST)
- topology/parameter entries for asphaltenes? jose correa (Fri Dec 26 2008 - 09:21:52 CST)
- Stupid question about compiling NAMD with cygwin on windows accomp lin (Thu Dec 25 2008 - 21:19:50 CST)
- Problems on SMD simulation ÕÅÓÂ (Thu Dec 25 2008 - 01:08:27 CST)
- CGMD parameters BIN ZHANG (Tue Dec 23 2008 - 20:06:32 CST)
- compiling namd on SGI Altix Blake Mertz (Tue Dec 23 2008 - 11:09:10 CST)
- tclforces: switch from md with external forces to standard md Vlad Cojocaru (Tue Dec 23 2008 - 09:01:36 CST)
- Re: tclforces: switch from md with external forces to standard md Peter Freddolino (Thu Jan 08 2009 - 13:38:05 CST)
- Re: tclforces: switch from md with external forces to standard md Jerome Henin (Fri Jan 09 2009 - 10:24:24 CST)
- Re: tclforces: switch from md with external forces to standard md Peter Freddolino (Fri Jan 09 2009 - 10:46:05 CST)
- Re: tclforces: switch from md with external forces to standard md Peter Freddolino (Fri Jan 09 2009 - 15:49:35 CST)
- Re: tclforces: switch from md with external forces to standard md Peter Freddolino (Fri Jan 09 2009 - 16:03:56 CST)
- Re: tclforces: switch from md with external forces to standard md Vlad Cojocaru (Mon Jan 12 2009 - 01:57:20 CST)
- Re: tclforces: switch from md with external forces to standard md Jerome Henin (Fri Jan 09 2009 - 10:24:24 CST)
- Re: tclforces: switch from md with external forces to standard md Peter Freddolino (Thu Jan 08 2009 - 13:38:05 CST)
- addforce on the com of a group of atoms and loadforces command Vlad Cojocaru (Tue Dec 23 2008 - 07:57:29 CST)
- Namd job terminates after ~10000+ itrations Sangamesh B (Tue Dec 23 2008 - 00:29:25 CST)
- (no subject) karthik s (Tue Dec 23 2008 - 00:07:39 CST)
- NAMD for Intel Xeon Cluster with MPICH DimitryASuplatov (Mon Dec 22 2008 - 06:33:48 CST)
- xsc file format Kyriakos Kachrimanis (Mon Dec 22 2008 - 03:24:46 CST)
- Problems with CUDA Build Christopher Share (Sun Dec 21 2008 - 23:58:47 CST)
- regarding protein-dna complex simulation please reply....... prasun kumar (Sun Dec 21 2008 - 19:30:07 CST)
- alchemical FEP question Nandhini Sokkalingam (Fri Dec 19 2008 - 21:44:52 CST)
- regarding protein-dna complex simulation prasun kumar (Fri Dec 19 2008 - 19:47:21 CST)
- entropy calculation hodak_at_chips.ncsu.edu (Fri Dec 19 2008 - 15:18:28 CST)
- filling hydrophobic cavity with... methane? Sebastian Stolzenberg (Thu Dec 18 2008 - 16:10:00 CST)
- Re: How to fix the Center of mass of protein when performing SMD? ÕÅÓÂ (Wed Dec 17 2008 - 22:06:14 CST)
- topology/parameter file for ligands bo baker (Wed Dec 17 2008 - 20:56:50 CST)
- angle deformation CHINDEA Vlad (Wed Dec 17 2008 - 17:00:49 CST)
- patch DISU to 2 residues jose correa (Wed Dec 17 2008 - 11:58:14 CST)
- parameter for compiling Ting Zhou (Wed Dec 17 2008 - 07:42:06 CST)
- Access to CVS Christopher Share (Tue Dec 16 2008 - 19:08:53 CST)
- failure in RATTLE Sangamesh B (Tue Dec 16 2008 - 08:20:24 CST)
- NAMD compile error itvasile_at_nipne.ro (Tue Dec 16 2008 - 10:43:20 CST)
- Unsure about current setting of Periodic Boundary Conditions Diego Alejandro Vargas (Tue Dec 16 2008 - 00:09:12 CST)
- top_all22_model.inp bo baker (Mon Dec 15 2008 - 22:50:07 CST)
- How to fix the Center of mass of protein when performing SMD? ÕÅÓÂ (Mon Dec 15 2008 - 21:54:20 CST)
- compiling latest CVS on altix L. Michel Espinoza-Fonseca (Sat Dec 13 2008 - 10:10:24 CST)
- To channel bond or not ? Nicholas M Glykos (Sat Dec 13 2008 - 04:33:02 CST)
- reg parameter of ions balaji nagarajan (Fri Dec 12 2008 - 22:43:41 CST)
- how to get 2 identical trajectories using NAMD in parallel Vlad Cojocaru (Fri Dec 12 2008 - 09:33:44 CST)
- Single topology FEP Sébastien Légaré (Thu Dec 11 2008 - 15:05:07 CST)
- Re: Loops in tclForcesScript BIN ZHANG (Thu Dec 11 2008 - 14:45:38 CST)
- Loops in tclForcesScript Yang, Lee Wei (Thu Dec 11 2008 - 12:01:08 CST)
- how to apply restraints for phi and psi for alpha helix regions Achani K. Yatawara (Thu Dec 11 2008 - 07:42:37 CST)
- water box getting deformed sunita gupta (Thu Dec 11 2008 - 07:06:30 CST)
- srand in a tclforces script Vlad Cojocaru (Thu Dec 11 2008 - 06:55:53 CST)
- FW: Multiplicity of parameters for improper bonds .............. of 1 exceeded. CHINDEA Vlad (Thu Dec 11 2008 - 06:17:20 CST)
- (no subject) CHINDEA Vlad (Thu Dec 11 2008 - 06:12:05 CST)
- DMF solvent parameters Austin B. Yongye (Wed Dec 10 2008 - 16:08:17 CST)
- POLL: free energy of conformational change Jerome Henin (Wed Dec 10 2008 - 10:25:14 CST)
- phi and psi restraints for 2 helix regions Achani K. Yatawara (Wed Dec 10 2008 - 07:13:57 CST)
- problem in solvating the protein sunita gupta (Wed Dec 10 2008 - 06:14:50 CST)
- minimization with amberff ramya narasimhan (Wed Dec 10 2008 - 01:47:34 CST)
- Reading multiple .log files Anirban Ghosh (Tue Dec 09 2008 - 22:42:15 CST)
- How to reverse the smd pcv pulling simulation Wang,Ying (Tue Dec 09 2008 - 16:49:29 CST)
- tcl forces/membranes David A. Horita (Tue Dec 09 2008 - 15:28:07 CST)
- Wrap ions? Rabab Toubar (Tue Dec 09 2008 - 10:56:07 CST)
- Increase the decimal points of energy output Yang, Lee Wei (Tue Dec 09 2008 - 05:14:10 CST)
- Coulombic virials Benjamin Roberts (Mon Dec 08 2008 - 22:14:00 CST)
- Output force acting on each atom in the system Yang, Lee Wei (Mon Dec 08 2008 - 09:10:26 CST)
- parameters and topology file needed for coarse-grain simulation sunita gupta (Mon Dec 08 2008 - 04:35:38 CST)
- TCL8.5? or Christopher Hartshorn (Sun Dec 07 2008 - 23:16:42 CST)
- CGMD timestep BIN ZHANG (Sun Dec 07 2008 - 14:44:23 CST)
- Equilibration simulation too slow. Diego Alejandro Vargas (Sun Dec 07 2008 - 09:59:35 CST)
- error in explicit membrane protein simulations gurvisha_at_leadinvent.com (Sat Dec 06 2008 - 04:11:50 CST)
- HP Cluster Platform 4000 Hannes Loeffler (Fri Dec 05 2008 - 07:52:02 CST)
- Energy conversation Alexander A. Vakhrushev (Fri Dec 05 2008 - 07:51:06 CST)
- output while tclforces active Vlad Cojocaru (Fri Dec 05 2008 - 02:46:10 CST)
- Electron density profile? BIN ZHANG (Fri Dec 05 2008 - 01:40:53 CST)
- regarding writemol2 jani sahil (Thu Dec 04 2008 - 23:16:49 CST)
- install namd on dell power edge 1900 Ramon Rocha (Thu Dec 04 2008 - 11:43:08 CST)
- Reading multiple .log files into one Anirban Ghosh (Thu Dec 04 2008 - 08:25:05 CST)
- create inositol molecule politr_at_huji.ac.il (Wed Dec 03 2008 - 10:48:38 CST)
- mpirun compilation for NAMD Neelanjana Sengupta (Wed Dec 03 2008 - 07:46:54 CST)
- Re: mpirun compilation for NAMD Giacomo Fiorin (Wed Dec 03 2008 - 10:42:44 CST)
- Re: mpirun compilation for NAMD Warner Yuen (Thu Dec 04 2008 - 12:08:37 CST)
- Re: mpirun compilation for NAMD Giacomo Fiorin (Thu Dec 04 2008 - 12:13:14 CST)
- Re: mpirun compilation for NAMD Warner Yuen (Thu Dec 04 2008 - 12:54:37 CST)
- Re: mpirun compilation for NAMD Axel Kohlmeyer (Fri Dec 05 2008 - 02:56:30 CST)
- Re: mpirun compilation for NAMD Neelanjana Sengupta (Thu Dec 04 2008 - 20:34:35 CST)
- Re: mpirun compilation for NAMD Axel Kohlmeyer (Fri Dec 05 2008 - 03:10:24 CST)
- Re: mpirun compilation for NAMD Warner Yuen (Thu Dec 04 2008 - 12:08:37 CST)
- Re: mpirun compilation for NAMD Giacomo Fiorin (Wed Dec 03 2008 - 10:42:44 CST)
- MacOSX 64bit binaries Christopher Hartshorn (Wed Dec 03 2008 - 01:34:26 CST)
- submit namd job in cluster Rudra Banerjee (Tue Dec 02 2008 - 23:04:29 CST)
- CGMD problem BIN ZHANG (Tue Dec 02 2008 - 11:10:34 CST)
- Help: do you have the top parameter of Gla Wang,Ying (Tue Dec 02 2008 - 10:27:56 CST)
- bash: namd2: command not found Sukesh Chandra Gain (Tue Dec 02 2008 - 00:31:42 CST)
- Modification of the NAMD forcefield functions ??? Maxim Paliy (Mon Dec 01 2008 - 13:39:31 CST)
- Errors on Missing Atoms for Some Bonds Taekyung Kwon (Sun Nov 30 2008 - 22:19:29 CST)
- Biotin-X charmm topology Taekyung Kwon (Sat Nov 29 2008 - 17:13:47 CST)
- SMD-Applied Forces and Analysis ÖÜÎIJý (Fri Nov 28 2008 - 02:27:24 CST)
- constraint failure problem. ydhuang2727 (Wed Nov 26 2008 - 20:54:30 CST)
- namd cvs compilation BIN ZHANG (Wed Nov 26 2008 - 18:55:07 CST)
- Re: namd cvs compilation BIN ZHANG (Wed Nov 26 2008 - 19:24:19 CST)
- Re: namd cvs compilation BIN ZHANG (Thu Nov 27 2008 - 01:00:14 CST)
- Re: namd cvs compilation Anirban Ghosh (Thu Nov 27 2008 - 02:27:57 CST)
- running namd on cluster Rudra Banerjee (Thu Nov 27 2008 - 04:25:18 CST)
- Re: namd cvs compilation BIN ZHANG (Thu Nov 27 2008 - 20:20:46 CST)
- Re: namd cvs compilation Anirban Ghosh (Thu Nov 27 2008 - 22:46:34 CST)
- Re: namd cvs compilation BIN ZHANG (Fri Nov 28 2008 - 00:11:14 CST)
- Re: namd cvs compilation Peter Freddolino (Sat Nov 29 2008 - 06:52:25 CST)
- Re: namd cvs compilation BIN ZHANG (Mon Dec 01 2008 - 11:59:39 CST)
- Re: namd cvs compilation Peter Freddolino (Mon Dec 01 2008 - 13:14:10 CST)
- Re: namd cvs compilation Peter Freddolino (Fri Nov 28 2008 - 21:10:36 CST)
- Re: namd cvs compilation BIN ZHANG (Thu Nov 27 2008 - 01:00:14 CST)
- Re: namd cvs compilation BIN ZHANG (Wed Nov 26 2008 - 19:24:19 CST)
- force potentials for residue-based CG Dolan, Michael (NIH/NIAID) [C] (Wed Nov 26 2008 - 13:36:51 CST)
- TIP4 water model NAMD Mehdi Bagheri-Hamaneh (Wed Nov 26 2008 - 10:28:25 CST)
- NAMD CVS Installation Anirban Ghosh (Wed Nov 26 2008 - 05:53:38 CST)
- RAM/node Alessio Alexiadis (Wed Nov 26 2008 - 05:37:17 CST)
- How do you keep atoms a fixed distance apart? timko_at_physics.usyd.edu.au (Wed Nov 26 2008 - 00:59:47 CST)
- Re: Compiling 8Core macs Christopher Hartshorn (Tue Nov 25 2008 - 15:28:51 CST)
- Re: vmd-l: CG bead definition BIN ZHANG (Tue Nov 25 2008 - 15:01:37 CST)
- MD-problems-GPCR in POPC bilayer jose correa (Tue Nov 25 2008 - 09:30:50 CST)
- Free energy calculation fixing the dihedrals Jagan Mohan (Tue Nov 25 2008 - 01:09:46 CST)
- Compiling 8Core macs Christopher Hartshorn (Mon Nov 24 2008 - 17:03:40 CST)
- NAMD with CUDA Status ? David McGiven (Mon Nov 24 2008 - 11:06:05 CST)
- NAMD with mpirun Neelanjana Sengupta (Mon Nov 24 2008 - 05:27:15 CST)
- build missing residues in pdb Anuradha Mittal (Sun Nov 23 2008 - 18:48:47 CST)
- regarding cgmd jani sahil (Sun Nov 23 2008 - 23:14:34 CST)
- Re- Loading .vel file in VMD dipti lele (Sun Nov 23 2008 - 19:18:06 CST)
- can the harmonic constraint parameters be changed between run or minimize? Chongbo Sun (Sun Nov 23 2008 - 14:03:39 CST)
- namdEnergy gives significantly different values from those in log file? Steven Samuel Plotkin (Sat Nov 22 2008 - 23:39:40 CST)
- Re: namdEnergy gives significantly different values from those in log file? Peter Freddolino (Sun Nov 23 2008 - 01:55:51 CST)
- Re: namdEnergy gives significantly different values from those in log file? Peter Freddolino (Sun Nov 23 2008 - 12:33:56 CST)
- Re: namdEnergy gives significantly different values from those in log file? Steven Samuel Plotkin (Mon Nov 24 2008 - 01:50:02 CST)
- Re: namdEnergy gives significantly different values from those in log file? Peter Freddolino (Mon Nov 24 2008 - 21:29:34 CST)
- Re: namdEnergy gives significantly different values from those in log file? Steven Samuel Plotkin (Wed Nov 26 2008 - 00:18:13 CST)
- Re: namdEnergy gives significantly different values from those in log file? Jerome Henin (Wed Nov 26 2008 - 10:16:12 CST)
- Re: namdEnergy gives significantly different values from those in log file? Peter Freddolino (Wed Nov 26 2008 - 12:10:37 CST)
- Re: namdEnergy gives significantly different values from those in log file? Steven Samuel Plotkin (Sat Nov 29 2008 - 21:39:07 CST)
- Re: namdEnergy gives significantly different values from those in log file? Peter Freddolino (Sat Nov 29 2008 - 23:12:01 CST)
- Re: namdEnergy gives significantly different values from those in log file? Steven Samuel Plotkin (Mon Nov 24 2008 - 01:50:02 CST)
- bond length in terminal patches CHINDEA Vlad (Sat Nov 22 2008 - 16:29:55 CST)
- Direction of steered molecular dynamics ÖÜÎIJý (Sat Nov 22 2008 - 08:39:51 CST)
- A way to check for non-unique coordinates? Diego Alejandro Vargas (Thu Nov 20 2008 - 23:15:58 CST)
- Loading .vel file in VMD dipti lele (Thu Nov 20 2008 - 23:03:42 CST)
- A way to check for non-unique coordinates? Diego Alejandro Vargas (Thu Nov 20 2008 - 21:22:21 CST)
- ERROR: Constraint failure in RATTLE algorithm for atom 872 ydhuang2727 (Thu Nov 20 2008 - 19:49:08 CST)
- namd latest CVS version on BluegeneP George Madalin Giambasu (Thu Nov 20 2008 - 16:05:13 CST)
- Fwd: How can I load two forcefied at the same time Wang,Ying (Thu Nov 20 2008 - 13:24:10 CST)
- H-bond occupancy in nucleic acids Tianjiao Wang (Thu Nov 20 2008 - 10:08:27 CST)
- namdplot Unmatched " error maria goranovic (Thu Nov 20 2008 - 08:50:52 CST)
- Regarding Installation Jagan Mohan (Thu Nov 20 2008 - 04:22:49 CST)
- pairlist i_upper mismatch! Diego Alejandro Vargas (Wed Nov 19 2008 - 22:28:41 CST)
- Re: pairlist i_upper mismatch! Peter Freddolino (Thu Nov 20 2008 - 09:03:56 CST)
- Re: pairlist i_upper mismatch! Diego Alejandro Vargas (Thu Nov 20 2008 - 10:52:34 CST)
- Re: pairlist i_upper mismatch! Peter Freddolino (Thu Nov 20 2008 - 10:56:30 CST)
- Re: pairlist i_upper mismatch! Diego Alejandro Vargas (Sat Nov 22 2008 - 00:20:25 CST)
- Re: pairlist i_upper mismatch! Schreiner Eduard (Sat Nov 22 2008 - 00:41:08 CST)
- Re: pairlist i_upper mismatch! Diego Alejandro Vargas (Sat Nov 22 2008 - 01:09:13 CST)
- Re: pairlist i_upper mismatch! Schreiner Eduard (Sat Nov 22 2008 - 01:47:01 CST)
- Re: pairlist i_upper mismatch! Floris Buelens (Sat Nov 22 2008 - 04:22:10 CST)
- Re: pairlist i_upper mismatch! Diego Alejandro Vargas (Thu Nov 20 2008 - 10:52:34 CST)
- Re: pairlist i_upper mismatch! Diego Alejandro Vargas (Sat Nov 22 2008 - 22:20:31 CST)
- Re: pairlist i_upper mismatch! Peter Freddolino (Thu Nov 20 2008 - 09:03:56 CST)
- TclBC - multiple iteration Chi-Cheng Chiu (Wed Nov 19 2008 - 12:15:48 CST)
- How to fix atoms during minimization? Anirban Ghosh (Wed Nov 19 2008 - 08:06:29 CST)
- FEP simulations? Christopher Hartshorn (Tue Nov 18 2008 - 13:19:13 CST)
- Re: FEP simulations? Jerome Henin (Tue Nov 18 2008 - 15:43:42 CST)
- FEP on charged residue mutation Sebastian Stolzenberg (Fri Nov 21 2008 - 16:22:45 CST)
- Re: FEP on charged residue mutation Jerome Henin (Fri Nov 21 2008 - 16:54:40 CST)
- Re: FEP on charged residue mutation Sebastian Stolzenberg (Sat Nov 22 2008 - 11:34:10 CST)
- Re: FEP on charged residue mutation Jerome Henin (Sat Nov 22 2008 - 11:57:11 CST)
- Re: FEP on charged residue mutation Sebastian Stolzenberg (Sat Nov 22 2008 - 12:14:57 CST)
- Re: FEP on charged residue mutation Jerome Henin (Sat Nov 22 2008 - 12:27:19 CST)
- Re: FEP on charged residue mutation Sebastian Stolzenberg (Sat Nov 22 2008 - 13:48:14 CST)
- Re: FEP on charged residue mutation Jerome Henin (Sat Nov 22 2008 - 16:30:52 CST)
- tclforce script in FEP: global variable Sebastian Stolzenberg (Tue Nov 25 2008 - 01:27:09 CST)
- Re: tclforce script in FEP: global variable Jerome Henin (Tue Nov 25 2008 - 08:57:24 CST)
- Re: Re: tclforce script in FEP: global variable Sebastian Stolzenberg (Tue Nov 25 2008 - 18:21:12 CST)
- Re: Re: tclforce script in FEP: global variable Jerome Henin (Tue Nov 25 2008 - 20:34:45 CST)
- Re: Re: tclforce script in FEP: global variable Sebastian Stolzenberg (Tue Nov 25 2008 - 23:53:44 CST)
- lithium parameters Sebastian Stolzenberg (Wed Dec 10 2008 - 19:11:47 CST)
- Re: lithium parameters Jawahar Neelankatan (Thu Dec 11 2008 - 10:24:39 CST)
- combine PMF/dual FEP -> correct free energies? Sebastian Stolzenberg (Thu Dec 11 2008 - 19:09:28 CST)
- Re: combine PMF/dual FEP -> correct free energies? Jerome Henin (Fri Dec 12 2008 - 11:10:14 CST)
- topology/parameter entries for methane? Sebastian Stolzenberg (Wed Dec 17 2008 - 18:08:25 CST)
- Re: topology/parameter entries for methane? Jerome Henin (Wed Dec 17 2008 - 20:25:32 CST)
- Re: topology/parameter entries for methane? Christophe.Chipot_at_edam.uhp-nancy.fr (Sat Dec 20 2008 - 05:15:12 CST)
- Re: FEP on charged residue mutation Sebastian Stolzenberg (Tue Nov 25 2008 - 19:30:08 CST)
- Re: FEP on charged residue mutation Jerome Henin (Tue Nov 25 2008 - 20:26:41 CST)
- Re: FEP on charged residue mutation Sebastian Stolzenberg (Tue Nov 25 2008 - 19:48:21 CST)
- Re: FEP simulations? Christopher Hartshorn (Mon Jan 05 2009 - 03:20:53 CST)
- FEP on charged residue mutation Sebastian Stolzenberg (Fri Nov 21 2008 - 16:22:45 CST)
- Re: FEP simulations? Jerome Henin (Tue Nov 18 2008 - 15:43:42 CST)
- periodic cell has become too small for original patch grid! ydhuang2727 (Tue Nov 18 2008 - 02:54:42 CST)
- restart sripad chandan (Mon Nov 17 2008 - 23:14:12 CST)
- FEP calculation of dimerization Christopher Hartshorn (Sun Nov 16 2008 - 23:45:05 CST)
- ABF:problems with calculating Free Energy Profile supram_at_nankai.edu.cn (Sun Nov 16 2008 - 20:55:39 CST)
- Re: langevinDamping Hyundeok Song (Sun Nov 16 2008 - 18:03:58 CST)
- Problems with minimization Diego Alejandro Vargas (Sat Nov 15 2008 - 10:57:23 CST)
- Re: Problems with minimization Christopher Gillespie (Sat Nov 15 2008 - 11:38:26 CST)
- Re: Problems with minimization Diego Alejandro Vargas (Sat Nov 15 2008 - 11:53:06 CST)
- Re: Problems with minimization Christopher Gillespie (Sat Nov 15 2008 - 12:10:46 CST)
- Re: Problems with minimization Peter Freddolino (Sat Nov 15 2008 - 12:43:56 CST)
- Re: Problems with minimization Diego Alejandro Vargas (Sun Nov 16 2008 - 00:28:53 CST)
- Re: Problems with minimization Diego Alejandro Vargas (Mon Nov 17 2008 - 20:54:14 CST)
- Re: Problems with minimization Diego Alejandro Vargas (Sat Nov 15 2008 - 11:53:06 CST)
- Re: Problems with minimization Christopher Gillespie (Sat Nov 15 2008 - 11:38:26 CST)
- How can I monitor the force during constant velocity SMD? wayj86 wayj86 (Sat Nov 15 2008 - 07:26:02 CST)
- langevinDamping Roman Petrenko (Fri Nov 14 2008 - 20:45:10 CST)
- constraint failure in RATTLE algorithm for atom 3205 ydhuang2727 (Fri Nov 14 2008 - 19:42:20 CST)
- NAMD Simulation error Anirban Ghosh (Fri Nov 14 2008 - 02:36:16 CST)
- NAMD Simulation error Anirban Ghosh (Wed Nov 12 2008 - 22:41:07 CST)
- Load balancing off Jonathan Bourne (Wed Nov 12 2008 - 12:20:25 CST)
- Force field parameters Rabab Toubar (Wed Nov 12 2008 - 10:27:58 CST)
- scalability problem on linux cluster Ruchi Sachdeva (Wed Nov 12 2008 - 08:28:09 CST)
- par-extraterms.inp file needed mahesh kulharia (Wed Nov 12 2008 - 04:07:32 CST)
- failure in RATTLE algorithm using the adaptive biasing force method steve.kaminski_at_mail.tu-berlin.de (Tue Nov 11 2008 - 13:43:51 CST)
- converting AMBER trajectory file to CHARMM trajectory file sunita gupta (Tue Nov 11 2008 - 04:37:27 CST)
- FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HT1 ramya narasimhan (Tue Nov 11 2008 - 03:23:43 CST)
- solvate using Helmut Grubmuller's SOLVATE and then VMD, then how to minimize properly! ydhuang2727 (Tue Nov 11 2008 - 02:30:40 CST)
- protein instability sripad chandan (Mon Nov 10 2008 - 21:27:18 CST)
- Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Mamta Mohan (Mon Nov 10 2008 - 10:50:57 CST)
- Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Peter Freddolino (Mon Nov 10 2008 - 11:26:05 CST)
- Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Mamta Mohan (Mon Nov 10 2008 - 13:39:18 CST)
- Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Peter Freddolino (Mon Nov 10 2008 - 13:52:11 CST)
- Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Mamta Mohan (Mon Nov 10 2008 - 14:20:49 CST)
- Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Peter Freddolino (Mon Nov 10 2008 - 20:02:10 CST)
- Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Mamta Mohan (Mon Nov 10 2008 - 13:48:49 CST)
- Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Mamta Mohan (Mon Nov 10 2008 - 13:39:18 CST)
- Non-standard amino acid Austin B. Yongye (Mon Nov 10 2008 - 17:05:01 CST)
- Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Peter Freddolino (Mon Nov 10 2008 - 11:26:05 CST)
- Error while using NAMD Marcus Batista (Sun Nov 09 2008 - 15:54:38 CST)
- impropers for aromatic residues CHINDEA Vlad (Sat Nov 08 2008 - 15:17:44 CST)
- Charm++ Fatal error ! Periodic cell has become too small for original patch grid! CHINDEA Vlad (Thu Nov 06 2008 - 17:40:35 CST)
- Re: Charm++ Fatal error ! Periodic cell has become too small for original patch grid! Joshua Adelman (Fri Nov 07 2008 - 11:31:59 CST)
- Re: Charm++ Fatal error ! Periodic cell has become too small for original patch grid! Dave Rogers (Fri Nov 07 2008 - 12:23:52 CST)
- Re: Charm++ Fatal error ! Periodic cell has become too small for original patch grid! Peter Freddolino (Fri Nov 07 2008 - 12:45:34 CST)
- Re: Charm++ Fatal error ! Periodic cell has become too small for original patch grid! Roman Petrenko (Fri Nov 07 2008 - 13:57:33 CST)
- Re: Charm++ Fatal error ! Periodic cell has become too small for original patch grid! Peter Freddolino (Fri Nov 07 2008 - 14:38:47 CST)
- Re: Charm++ Fatal error ! Periodic cell has become too small for original patch grid! Dave Rogers (Fri Nov 07 2008 - 12:23:52 CST)
- Re: Charm++ Fatal error ! Periodic cell has become too small for original patch grid! Joshua Adelman (Fri Nov 07 2008 - 11:31:59 CST)
- generating psf & energy calculation for unusual amino acid - Aib balaji nagarajan (Thu Nov 06 2008 - 21:57:17 CST)
- PME non-zero charge Roman Petrenko (Thu Nov 06 2008 - 15:07:56 CST)
- NAMD2.6 appears to be freezing at or during load balancing Jonathan Bourne (Thu Nov 06 2008 - 12:33:23 CST)
- segmentation fault? BIN ZHANG (Wed Nov 05 2008 - 15:58:58 CST)
- Add ions ydhuang2727 (Wed Nov 05 2008 - 02:16:33 CST)
- Re: building namd on CRAY-XT3 BIN ZHANG (Wed Nov 05 2008 - 00:16:34 CST)
- building namd on CRAY-XT3 BIN ZHANG (Tue Nov 04 2008 - 13:38:35 CST)
- Atoms moving too fast OR constraint failure in RATTLE algorithm Diego Alejandro Vargas (Tue Nov 04 2008 - 12:34:00 CST)
- Re: Atoms moving too fast OR constraint failure in RATTLE algorithm Joshua Adelman (Tue Nov 04 2008 - 12:58:44 CST)
- How can I specify an exact initial velocity? wayj86 wayj86 (Tue Nov 04 2008 - 02:29:07 CST)
- log file problem ydhuang2727 (Mon Nov 03 2008 - 19:57:08 CST)
- Fw: NAMD mail bounce problem. Mamta Mohan (Mon Nov 03 2008 - 12:35:46 CST)
- Approach energy with SMD Austin B. Yongye (Mon Nov 03 2008 - 11:01:26 CST)
- multiple simulations sripad chandan (Sun Nov 02 2008 - 22:32:11 CST)
- (no subject) Bertrand P. S. Russell (Sat Nov 01 2008 - 20:50:16 CDT)
- AMBER ff99SB on NAMD Luis Cunha (Sat Nov 01 2008 - 19:43:30 CDT)
- NAMD2.6 repeatedly freezing on new desktop Jonathan Bourne (Sat Nov 01 2008 - 16:03:53 CDT)
- unsubscribe Bertrand P. S. Russell (Fri Oct 31 2008 - 23:10:48 CDT)
- Two questions about free dynamics simulation wayj86 wayj86 (Fri Oct 31 2008 - 21:46:25 CDT)
- Could I do the equilibration again with the same dcd file obtained? wayj86 wayj86 (Thu Oct 30 2008 - 20:40:09 CDT)
- combining 2 dcd files into one Rabab Toubar (Thu Oct 30 2008 - 15:20:34 CDT)
- Problem with temperature increase in equilibration. Diego Alejandro Vargas (Thu Oct 30 2008 - 11:14:54 CDT)
- ions behavior in protein-water box: Emanuelle Bachelet (Wed Oct 29 2008 - 13:44:59 CDT)
- Re: ions behavior in protein-water box: Christopher Gillespie (Wed Oct 29 2008 - 15:05:19 CDT)
- Re: ions behavior in protein-water box: Emanuelle Bachelet (Wed Oct 29 2008 - 16:56:10 CDT)
- Re: ions behavior in protein-water box: Christopher Gillespie (Wed Oct 29 2008 - 17:12:23 CDT)
- Re: ions behavior in protein-water box: Axel Kohlmeyer (Wed Oct 29 2008 - 17:39:03 CDT)
- Re: ions behavior in protein-water box: Emanuelle Bachelet (Thu Oct 30 2008 - 12:24:27 CDT)
- Re: ions behavior in protein-water box: Joshua Adelman (Thu Oct 30 2008 - 13:40:45 CDT)
- Re: ions behavior in protein-water box: Christopher Gillespie (Thu Oct 30 2008 - 13:50:38 CDT)
- Re: ions behavior in protein-water box: Emanuelle Bachelet (Thu Oct 30 2008 - 14:38:13 CDT)
- Re: ions behavior in protein-water box: Leandro Martínez (Thu Oct 30 2008 - 17:02:16 CDT)
- Re: ions behavior in protein-water box: Emanuelle Bachelet (Fri Oct 31 2008 - 12:08:53 CDT)
- Re: ions behavior in protein-water box: Emanuelle Bachelet (Wed Oct 29 2008 - 16:56:10 CDT)
- Re: ions behavior in protein-water box: Christopher Gillespie (Wed Oct 29 2008 - 15:05:19 CDT)
- Why there is a bond between the two Hydrogens of the TIP3P water in Amber force field? Ming (Wed Oct 29 2008 - 10:20:31 CDT)
- Re: Why there is a bond between the two Hydrogens of the TIP3P water in Amber force field? Purushottam Dixit (Wed Oct 29 2008 - 10:36:42 CDT)
- ABF backbone dihedral Sébastien Légaré (Tue Oct 28 2008 - 11:44:21 CDT)
- Backbone dihedral ABF Sébastien Légaré (Tue Oct 28 2008 - 11:50:02 CDT)
- ABF - using gyration Subramanian Vaitheeswaran (Tue Oct 28 2008 - 10:18:08 CDT)
- Re: ABF - using gyration Jerome Henin (Tue Oct 28 2008 - 11:52:49 CDT)
- dcd to pdb conversion Ayşe Özlem Aykut (Mon Oct 27 2008 - 03:28:16 CDT)
- applying stress to study elasticity Lam Nguyen (Fri Oct 24 2008 - 11:06:35 CDT)
- CG Name Prefix Problem Anirban Ghosh (Fri Oct 24 2008 - 00:24:58 CDT)
- How to keep Total Energy constant when an external force is added? Fred (Rui FENG) (Wed Oct 22 2008 - 22:48:43 CDT)
- Membrane Simulations Anshu Bhatia (Wed Oct 22 2008 - 20:04:38 CDT)
- Non Bonded Paramters abhijit ramachandran (Tue Oct 21 2008 - 17:25:04 CDT)
- Calcium ion binding protein vsweta_at_iastate.edu (Tue Oct 21 2008 - 16:27:31 CDT)
- fixedAtoms may not be enabled in a script Christopher Hartshorn (Tue Oct 21 2008 - 10:54:17 CDT)
- restart_minimization sripad chandan (Tue Oct 21 2008 - 05:30:12 CDT)
- Re: from NPT to NVT Hiroaki Maekawa (Mon Oct 20 2008 - 12:00:46 CDT)
- NVT/NPT pressures w fixed particles Arturas Ziemys (Mon Oct 20 2008 - 10:03:43 CDT)
- Inquire on gradual temperature increase. Diego Alejandro Vargas (Mon Oct 20 2008 - 08:59:46 CDT)
- rms gradient sripad chandan (Mon Oct 20 2008 - 04:59:07 CDT)
- How to set values for cellBasisVector and PMEGridSize properly ydhuang2727 (Mon Oct 20 2008 - 03:00:15 CDT)
- restart PMF: grow phase required? "lambdaRef"? more documentation on NAMD PMF? Sebastian Stolzenberg (Sun Oct 19 2008 - 13:43:56 CDT)
- Atom velocities too high. Diego Alejandro Vargas (Sun Oct 19 2008 - 09:59:10 CDT)
- How can I calculate the distance between two atoms frame by frame? wayj86 wayj86 (Sat Oct 18 2008 - 21:15:25 CDT)
- Re: How can I calculate the distance between two atoms frame by frame? Axel Kohlmeyer (Sat Oct 18 2008 - 22:07:13 CDT)
- Re: How can I calculate the distance between two atoms frame by frame? Grace Brannigan (Sat Oct 18 2008 - 23:05:45 CDT)
- Re: How can I calculate the distance between two atoms frame by frame? Jerome Henin (Sun Oct 19 2008 - 09:51:51 CDT)
- from NPT to NVT Hiroaki Maekawa (Fri Oct 17 2008 - 16:37:16 CDT)
- RE: Using NAMD to calculate pair energy with many subset permutations brmorgan_at_clarku.edu (Fri Oct 17 2008 - 09:39:05 CDT)
- right_protocal sripad chandan (Fri Oct 17 2008 - 06:02:54 CDT)
- restraint on a group of atoms at their center of mass? Dan W. (Thu Oct 16 2008 - 14:16:19 CDT)
- Error while running NPT Simulation Nd S (Thu Oct 16 2008 - 12:44:50 CDT)
- Pressure related issue Anirban Ghosh (Wed Oct 15 2008 - 08:23:29 CDT)
- Full Electrostatic Calculations on Protein in Vacuo MIke S (Thu Oct 16 2008 - 02:07:29 CDT)
- ERROR: DIDN'T FIND "NATOM" IN PSF FILE Diego Alejandro Vargas (Wed Oct 15 2008 - 23:12:01 CDT)
- Density Calculation Nd S (Wed Oct 15 2008 - 22:25:57 CDT)
- Getting total energy of system + pressure and temperature bath. Audrey Salazar (Wed Oct 15 2008 - 16:23:12 CDT)
- Using NAMD to calculate pair energy with many subset permutations brmorgan_at_clarku.edu (Wed Oct 15 2008 - 13:08:42 CDT)
- Quantitative Test for Equilibration of Data Time Series Joshua Adelman (Wed Oct 15 2008 - 12:06:00 CDT)
- megatest test failure/MPI problem Meij, Henk (Wed Oct 15 2008 - 10:14:48 CDT)
- How to choose force field? Diego Alejandro Vargas (Tue Oct 14 2008 - 23:34:20 CDT)
- Re: Error with External Electric Filed module Ramya Gamini (Tue Oct 14 2008 - 17:08:39 CDT)
- Membrane Simulations Anshu Bhatia (Tue Oct 14 2008 - 14:05:55 CDT)
- Error with External Electric Filed module Devendra (Tue Oct 14 2008 - 10:39:05 CDT)
- Re: FEP: How check equilibration sufficiency? calculate dG? Floris Buelens (Tue Oct 14 2008 - 02:45:50 CDT)
- Constraints protocol Kamilla Kopec (Mon Oct 13 2008 - 09:41:30 CDT)
- pressure calculation Matthew Ambrosia (Mon Oct 13 2008 - 05:11:06 CDT)
- Query Regarding FEP tutorial: NPT or NVT? mon_sharma_at_research.iiit.ac.in (Sat Oct 11 2008 - 16:33:04 CDT)
- PSF of Tryptophane methyl ester CHINDEA Vlad (Sat Oct 11 2008 - 11:43:43 CDT)
- velocities Magnus Heltstrom (Sat Oct 11 2008 - 11:00:54 CDT)
- Re: restarting issue BIN ZHANG (Fri Oct 10 2008 - 15:00:36 CDT)
- restarting issue BIN ZHANG (Fri Oct 10 2008 - 14:42:43 CDT)
- embedding protein in membrane jose correa (Fri Oct 10 2008 - 07:24:36 CDT)
- charmrun socket error David A. Horita (Thu Oct 09 2008 - 13:49:21 CDT)
- FEP: delta_G, memory of Hamiltonians corresponding to last G value? Sebastian Stolzenberg (Thu Oct 09 2008 - 14:10:20 CDT)
- swig wrapping c++ code on nersc BIN ZHANG (Thu Oct 09 2008 - 11:30:12 CDT)
- problems with combine.tcl jose correa (Wed Oct 08 2008 - 20:21:12 CDT)
- Constant z axis Nd S (Wed Oct 08 2008 - 19:59:43 CDT)
- embedding protein in membrane jose correa (Wed Oct 08 2008 - 09:08:12 CDT)
- Use tclforces to find systematic forces on fixed atoms? Bill K (Tue Oct 07 2008 - 16:20:44 CDT)
- RE: Problems compiling NAMD Jesper Soerensen (Fri Oct 03 2008 - 15:50:37 CDT)
- MD performance on 10 GBit/s or 20Gbit/s infiniband Himanshu Khandelia (Mon Oct 06 2008 - 09:08:35 CDT)
- firsttimestep question Dong Xu (Mon Oct 06 2008 - 00:00:46 CDT)
- equilibration of solvent box and pressure Hiroaki Maekawa (Sun Oct 05 2008 - 22:10:49 CDT)
- (no subject) CHINDEA Vlad (Sun Oct 05 2008 - 15:27:31 CDT)
- Problems compiling NAMD Jesper Soerensen (Fri Oct 03 2008 - 06:54:20 CDT)
- Re: Problems compiling NAMD Alexander A. Vakhrushev (Fri Oct 03 2008 - 12:44:57 CDT)
- Re: Problems compiling NAMD Jesper Soerensen (Mon Oct 06 2008 - 09:54:25 CDT)
- Re: Problems compiling NAMD Alexander A. Vakhrushev (Mon Oct 06 2008 - 11:00:38 CDT)
- Re: Problems compiling NAMD Jesper Soerensen (Tue Oct 07 2008 - 03:50:50 CDT)
- Re: Problems compiling NAMD Alexander A. Vakhrushev (Tue Oct 07 2008 - 05:04:47 CDT)
- Re: Problems compiling NAMD Axel Kohlmeyer (Tue Oct 07 2008 - 11:54:21 CDT)
- RE: Problems compiling NAMD Jesper Sørensen (Tue Oct 07 2008 - 17:19:44 CDT)
- RE: Problems compiling NAMD Axel Kohlmeyer (Tue Oct 07 2008 - 18:44:06 CDT)
- RE: Problems compiling NAMD Philip Peartree (Wed Oct 08 2008 - 06:03:06 CDT)
- RE: Problems compiling NAMD Jesper Soerensen (Wed Oct 08 2008 - 06:23:16 CDT)
- Re: Problems compiling NAMD Jesper Soerensen (Mon Oct 06 2008 - 09:54:25 CDT)
- Re: Problems compiling NAMD Alexander A. Vakhrushev (Fri Oct 03 2008 - 12:44:57 CDT)
- unknown residue LIP jose correa (Fri Oct 03 2008 - 12:07:24 CDT)
- Re: vmd-l: TAB key in vmd terminal BIN ZHANG (Fri Oct 03 2008 - 11:04:02 CDT)
- Problem with creating psf file from structure made by inorganic builder Anneta Tzampazi (Fri Oct 03 2008 - 04:43:19 CDT)
- error in atom type Rudra Banerjee (Thu Oct 02 2008 - 23:03:30 CDT)
- (no subject) Rudra Banerjee (Thu Oct 02 2008 - 23:01:25 CDT)
- PMEGridSize Rabab Toubar (Thu Oct 02 2008 - 13:55:04 CDT)
- Re: PMEGridSize Roman Petrenko (Thu Oct 02 2008 - 15:22:49 CDT)
- Re: PMEGridSize Rabab Toubar (Fri Oct 03 2008 - 15:22:19 CDT)
- Re: PMEGridSize JC Gumbart (Fri Oct 03 2008 - 21:53:25 CDT)
- Re: PMEGridSize Rabab Toubar (Mon Oct 06 2008 - 10:51:27 CDT)
- Re: PMEGridSize Chris Harrison (Fri Oct 10 2008 - 00:37:59 CDT)
- Re: PMEGridSize Rabab Toubar (Fri Oct 10 2008 - 08:32:18 CDT)
- Re: PMEGridSize V.Ovchinnikov (Fri Oct 10 2008 - 09:49:12 CDT)
- RE: PMEGridSize JC Gumbart (Sat Oct 11 2008 - 14:44:16 CDT)
- Re: PMEGridSize Chris Harrison (Sat Oct 11 2008 - 16:52:03 CDT)
- RE: PMEGridSize JC Gumbart (Sat Oct 11 2008 - 01:01:58 CDT)
- RE: PMEGridSize Rabab Toubar (Thu Jul 23 2009 - 15:13:03 CDT)
- Re: PMEGridSize Chris Harrison (Thu Jul 23 2009 - 16:52:06 CDT)
- Re: PMEGridSize JC Gumbart (Thu Jul 23 2009 - 19:08:52 CDT)
- Re: PMEGridSize Rabab Toubar (Fri Oct 03 2008 - 15:22:19 CDT)
- Re: PMEGridSize Roman Petrenko (Thu Oct 02 2008 - 15:22:49 CDT)
- psf generation for a small non-peptide molecule - again CHINDEA Vlad (Wed Oct 01 2008 - 16:38:27 CDT)
- DCD file format Santanu Chatterjee (Wed Oct 01 2008 - 13:35:25 CDT)
- Re: DCD file format Dave Rogers (Wed Oct 01 2008 - 14:17:10 CDT)
- Re: DCD file format Jerome Henin (Wed Oct 01 2008 - 14:38:35 CDT)
- Re: DCD file format Audrey Salazar (Wed Oct 01 2008 - 15:04:28 CDT)
- Re: DCD file format Alexander A. Vakhrushev (Wed Oct 01 2008 - 23:43:12 CDT)
- Re: DCD file format Andrew Emerson (Thu Oct 02 2008 - 02:32:08 CDT)
- intramolecular LJ parameters Hamsa Priya Mohana sundaram (Wed Oct 01 2008 - 12:19:56 CDT)
- autopsf and hydrogen-sites Christine Horejs DI (Wed Oct 01 2008 - 04:09:44 CDT)
- How to compute interaction energies between individual amino acid residues Jemmy Hu (Tue Sep 30 2008 - 11:24:33 CDT)
- Simple query dipti lele (Tue Sep 30 2008 - 04:33:24 CDT)
- Cyclopeptide: connectivity between the first and last residues List (Mon Sep 29 2008 - 12:52:14 CDT)
- asphaltene parameters jose correa (Mon Sep 29 2008 - 08:55:30 CDT)
- How to apply velocity to the entire system with COMmotion enabled Yinglong Miao (Mon Sep 29 2008 - 08:43:38 CDT)
- namd 2.5 compilation error Dong Xu (Sun Sep 28 2008 - 01:53:14 CDT)
- Running Multiple TMD simultaneously Joshua Adelman (Sat Sep 27 2008 - 14:57:09 CDT)
- minimization jose correa (Thu Sep 25 2008 - 20:11:36 CDT)
- psf generation for a small non-peptide molecule CHINDEA Vlad (Thu Sep 25 2008 - 16:18:40 CDT)
- OXT in pdb file Rabab Toubar (Thu Sep 25 2008 - 13:38:06 CDT)
- patch LINK - cyclizing a protein Rabab Toubar (Thu Sep 25 2008 - 13:34:19 CDT)
- membrane jose correa (Thu Sep 25 2008 - 09:08:11 CDT)
- How to use bigdcd on a trajectory while skipping first 1000 frames maria goranovic (Thu Sep 25 2008 - 04:42:29 CDT)
- membrane jose correa (Wed Sep 24 2008 - 18:43:55 CDT)
- Managing Log files Nd S (Wed Sep 24 2008 - 11:52:58 CDT)
- Periodic BCs Navdeep (Tue Sep 23 2008 - 17:38:52 CDT)
- restarting heating protocol problem: Parminder Mankoo (Tue Sep 23 2008 - 12:47:42 CDT)
- Membrane potential Lea Vinther Thøgersen (Tue Sep 23 2008 - 05:00:54 CDT)
- restarting heating protocol problem: Parminder Mankoo (Tue Sep 23 2008 - 12:55:42 CDT)
- Monte Carlo with NAMD Neelanjana Sengupta (Tue Sep 23 2008 - 10:50:29 CDT)
- solvate a molecule Rudra Banerjee (Tue Sep 23 2008 - 00:01:16 CDT)
- Namd water density jouko_at_uchicago.edu (Mon Sep 22 2008 - 21:36:11 CDT)
- TCL force BIN ZHANG (Mon Sep 22 2008 - 20:40:59 CDT)
- Re: TCL force Peter Freddolino (Tue Sep 23 2008 - 00:37:01 CDT)
- Re: TCL force BIN ZHANG (Tue Sep 23 2008 - 00:43:52 CDT)
- Re: TCL force Peter Freddolino (Tue Sep 23 2008 - 09:05:16 CDT)
- Re: TCL force BIN ZHANG (Tue Sep 23 2008 - 11:20:40 CDT)
- Re: TCL force Peter Freddolino (Tue Sep 23 2008 - 23:27:31 CDT)
- Re: TCL force BIN ZHANG (Wed Sep 24 2008 - 14:23:38 CDT)
- Re: TCL force Peter Freddolino (Thu Sep 25 2008 - 08:15:30 CDT)
- Re: TCL force Chi-Cheng Chiu (Wed Sep 24 2008 - 10:36:34 CDT)
- Re: TCL force Chi-Cheng Chiu (Wed Sep 24 2008 - 10:42:10 CDT)
- Re: TCL force BIN ZHANG (Tue Sep 23 2008 - 00:43:52 CDT)
- Re: TCL force Peter Freddolino (Tue Sep 23 2008 - 00:37:01 CDT)
- Re: need help on CG modelling Nicolas Sapay (Mon Sep 22 2008 - 12:34:47 CDT)
- Compile NAMD on Bluegene Yang Gao (Mon Sep 22 2008 - 10:37:58 CDT)
- carma v.0.9 Nicholas M Glykos (Mon Sep 22 2008 - 05:52:23 CDT)
- need help on CG modelling Liao Chuan (Mon Sep 22 2008 - 03:23:02 CDT)
- adjusted background load Roman Petrenko (Sat Sep 20 2008 - 10:13:08 CDT)
- Replica Exhange error: POSIX EINTR {interrupted system call} Dirar Homouz (Sat Sep 20 2008 - 04:11:55 CDT)
- Restarting a Simulation & Langevin Anirban Ghosh (Fri Sep 19 2008 - 08:12:34 CDT)
- psfgen Magnus Heltstrom (Fri Sep 19 2008 - 06:42:32 CDT)
- counting gas molecules inside the nanotube mishacat_at_udm.ru (Thu Sep 18 2008 - 06:52:51 CDT)
- Calcium ion-Protein Binding MIke S (Thu Sep 18 2008 - 14:13:34 CDT)
- Can I use "vecnorm" in the tclforce scripts? Ming (Thu Sep 18 2008 - 08:58:19 CDT)
- Re: convergence of abf Eric H. Lee (Thu Sep 18 2008 - 05:19:49 CDT)
- velocity DCD data retrieval Matthew Ambrosia (Wed Sep 17 2008 - 23:02:35 CDT)
- Oligomer Nejo (Wed Sep 17 2008 - 19:28:18 CDT)
- Calcium ions and psfgen MIke S (Wed Sep 17 2008 - 16:53:16 CDT)
- config files no longer working after software 'upgrades' Irene Newhouse (Tue Sep 16 2008 - 18:18:43 CDT)
- TCL Forces : OUT OF MEMORY BIN ZHANG (Fri Sep 12 2008 - 13:38:17 CDT)
- convergence of abf Jorgen Simonsen (Fri Sep 12 2008 - 10:03:17 CDT)
- parameter file to make cholesterol psf file peach gil (Wed Sep 10 2008 - 17:39:59 CDT)
- Regarding REMD jani sahil (Wed Sep 10 2008 - 00:04:19 CDT)
- trifluoroethanol (TFE) solvent Roman Petrenko (Tue Sep 09 2008 - 19:30:06 CDT)
- NAMD vs. CHARMM. Is complete correspondence possible? Niels Johan Christensen (Tue Sep 09 2008 - 14:18:21 CDT)
- Questions concerning NAMD mxenos_at_notes.cc.sunysb.edu (Tue Sep 09 2008 - 10:26:55 CDT)
- How to retrieve IC50 of a specific compound from NCBI? Ming (Tue Sep 09 2008 - 03:54:38 CDT)
- vmd-l: How to generate more segments? mishacat_at_udm.ru (Tue Sep 09 2008 - 01:30:05 CDT)
- restarting a simulation Raul Araya (Mon Sep 08 2008 - 17:47:35 CDT)
- Fwd: convergence of abf Eric H. Lee (Mon Sep 08 2008 - 14:45:53 CDT)
- FATAL ERROR: chdir() failed! LAM NGUYEN (Sat Sep 06 2008 - 14:56:57 CDT)
- psfgen: more problem Rudra Banerjee (Mon Sep 08 2008 - 13:30:31 CDT)
- convergence of abf Jorgen Simonsen (Mon Sep 08 2008 - 09:16:20 CDT)
- psf gen Rudra Banerjee (Sun Sep 07 2008 - 07:21:22 CDT)
- Compile NAMD on MIPS cpu(Loongson 2F) Guo Zhi (Fri Sep 05 2008 - 23:23:38 CDT)
- Coarse grained model force fields Myunggi Yi (Thu Sep 04 2008 - 14:01:49 CDT)
- vdW parameter Diego Alejandro Vargas (Wed Sep 03 2008 - 00:02:22 CDT)
- minimization warning and errors Lam T Nguyen (Tue Sep 02 2008 - 13:22:14 CDT)
- Platinum paramaters Neelanjana Sengupta (Mon Sep 01 2008 - 08:13:41 CDT)
- topology file for 2 sugar rings connected 1-1 between them politr_at_huji.ac.il (Sun Aug 31 2008 - 07:09:20 CDT)
- monitor a distance between two molecules me00109_at_cc.uoi.gr (Sat Aug 30 2008 - 18:06:11 CDT)
- COOH patch? MIke S (Sat Aug 30 2008 - 17:24:20 CDT)
- conskfile Shultz, Jack (Sat Aug 30 2008 - 12:46:29 CDT)
- Re: conskfile Axel Kohlmeyer (Sat Aug 30 2008 - 13:33:07 CDT)
- Constraint failure & velocity problem Shultz, Jack (Tue Sep 02 2008 - 13:40:09 CDT)
- Re: Constraint failure & velocity problem Peter Freddolino (Tue Sep 02 2008 - 14:00:41 CDT)
- Re: Constraint failure & velocity problem bo liu (Wed Sep 03 2008 - 00:08:15 CDT)
- RE: Constraint failure & velocity problem Shultz, Jack (Wed Sep 03 2008 - 20:13:24 CDT)
- Re: Constraint failure & velocity problem bo liu (Thu Sep 04 2008 - 00:26:14 CDT)
- Constraint failure & velocity problem Shultz, Jack (Tue Sep 02 2008 - 13:40:09 CDT)
- Re: conskfile Axel Kohlmeyer (Sat Aug 30 2008 - 13:33:07 CDT)
- Trouble with params file when trying to perform basic dynamics with alanine. Diego Alejandro Vargas (Fri Aug 29 2008 - 23:11:03 CDT)
- nvidia and namd Jorgen Simonsen (Fri Aug 29 2008 - 10:21:17 CDT)
- NPT enzemble and ABF Jorgen Simonsen (Fri Aug 29 2008 - 07:07:39 CDT)
- TXT program editor Alejandro Ortega (Thu Aug 28 2008 - 14:43:14 CDT)
- Re: vmd-l: TXT program editor Peter Freddolino (Thu Aug 28 2008 - 15:06:53 CDT)
- Re: vmd-l: TXT program editor Axel Kohlmeyer (Thu Aug 28 2008 - 15:50:21 CDT)
- Re: TXT program editor Giovanni Bellesia (Thu Aug 28 2008 - 16:21:03 CDT)
- Re: vmd-l: TXT program editor Sabuj Pattanayek (Thu Aug 28 2008 - 17:03:11 CDT)
- NAMD compilation / TACC Ranger Arturas Ziemys (Thu Aug 28 2008 - 11:25:14 CDT)
- PME questions Lam T Nguyen (Thu Aug 28 2008 - 10:58:54 CDT)
- diffusion coefficient from rmsd Rudra Banerjee (Wed Aug 27 2008 - 21:55:28 CDT)
- corrupt DCD file Forbes, Jeff (NIH/NIAMS) [E] (Wed Aug 27 2008 - 16:54:07 CDT)