Amber Archive Oct 2001: By Thread

Re: LINMIN Failure Michael Jakusch (Mon Oct 01 2001 - 08:17:17 PDT)
Possible error in AMBER parm94 file? John D. Chodera (Mon Oct 01 2001 - 17:01:37 PDT)
GB and Ions, 2nd try Andreas Svrcek-Seiler (Tue Oct 02 2001 - 08:43:39 PDT)
prowat test difficulties C. Singer (Tue Oct 02 2001 - 11:37:39 PDT)
RE: Binary mdcrd Halima Amer (Tue Oct 02 2001 - 23:43:41 PDT)
Re: problem with ambpdb Bill Ross (Wed Oct 03 2001 - 01:16:23 PDT)
Temperature and pressure couplings Filip Lankas (Wed Oct 03 2001 - 08:38:56 PDT)
- Re: Temperature and pressure couplings David Case (Wed Oct 03 2001 - 08:57:33 PDT)
- NAN errors during production runs Oliver Zerbe (Wed Oct 03 2001 - 09:45:10 PDT)
- ?s: Xeon vs. Athlon, latency R. M. Fesinmeyer (Wed Oct 03 2001 - 20:36:38 PDT)
  - RE: Xeon vs. Athlon, latency Yong Duan (Thu Oct 04 2001 - 10:19:29 PDT)
  - Re: ?s: Xeon vs. Athlon, latency Stephane (Fri Oct 05 2001 - 01:34:15 PDT)
  - post-processing of energy analysis Katherine Wallis Abold (Sun Oct 07 2001 - 13:58:30 PDT)
  - [Fwd: ?s: Xeon vs. Athlon, latency] Stephane (Mon Oct 08 2001 - 00:43:24 PDT)
  - NPSCAL parameter Nikolai Smolin (Mon Oct 08 2001 - 04:20:24 PDT)
  - Amber 6 MDCRD Files > 2GB in 32 bit Linux. Ross Walker (Mon Oct 08 2001 - 04:49:14 PDT)
  - analysis problem Eoin Galligan (Mon Oct 08 2001 - 06:12:22 PDT)
  - Re: ?s: Xeon vs. Athlon, latency R. M. Fesinmeyer (Mon Oct 08 2001 - 10:15:39 PDT)
Re: NPSCAL parameter Bill Ross (Mon Oct 08 2001 - 08:36:10 PDT)
RESP charges Eva Darian (Mon Oct 08 2001 - 14:44:16 PDT)
- Re: RESP charges Lepsa (Tue Oct 09 2001 - 00:56:49 PDT)
  - RESP charges (correction) Eva Darian (Tue Oct 09 2001 - 08:54:49 PDT)
    - Re: RESP charges (correction) Lepsa (Wed Oct 10 2001 - 00:15:53 PDT)
    - MM-PBSA; E(internal) Michal Otyepka (Wed Oct 10 2001 - 09:58:19 PDT)
    - P4 benchmarks posted Robert Matthew Fesinmeyer (Thu Oct 11 2001 - 13:10:14 PDT)
    - 5-methyl deoxycytosine parameters Jake Isaacs (Fri Oct 12 2001 - 06:13:59 PDT)
    - parameters Didier Rognan (Fri Oct 12 2001 - 09:12:37 PDT)
    - energy decomposition Elizabeth K. White (Sat Oct 13 2001 - 06:51:40 PDT)
    - re: energy decomposition Bill Ross (Sat Oct 13 2001 - 12:10:18 PDT)
    - trajectory analysis Sue Heavner (Sat Oct 13 2001 - 12:26:41 PDT)
    - Re: RESP charges (correction) Lepsa (Wed Oct 31 2001 - 08:01:30 PST)
  - ISTAR option and performance Anton B. Guliaev (Tue Oct 09 2001 - 10:39:10 PDT)
    - Re: ISTAR option and performance Jarrod Smith (Tue Oct 09 2001 - 11:30:22 PDT)
Code modification. John Finke (Mon Oct 08 2001 - 16:16:44 PDT)
Re: trajectory analysis Bill Ross (Sat Oct 13 2001 - 12:50:04 PDT)
adding water Rozita Dara (Sat Oct 13 2001 - 19:40:22 PDT)
Re: adding water Bill Ross (Sat Oct 13 2001 - 21:44:47 PDT)
Re: Can amber calculate the gibbs perturb energy when a ligand added a group Bill Ross (Sat Oct 13 2001 - 21:50:14 PDT)
torsional profile with MD Giulio Rastelli (Mon Oct 15 2001 - 09:17:34 PDT)
- Re: torsional profile with MD Bill Ross (Mon Oct 15 2001 - 10:17:12 PDT)
- ANAL Elizabeth K. White (Mon Oct 15 2001 - 10:45:18 PDT)
Re: torsional profile with MD Bill Ross (Mon Oct 15 2001 - 10:12:21 PDT)
Re: ANAL Bill Ross (Mon Oct 15 2001 - 11:17:23 PDT)
problem in a short MD with protein fixed dwang (Tue Oct 16 2001 - 18:00:26 PDT)
- Re: problem in a short MD with protein fixed Michael G Cooney (Wed Oct 17 2001 - 11:52:30 PDT)
- possible bug in carnal in AMBER5 Michael G Cooney (Wed Oct 17 2001 - 14:00:01 PDT)
Amber6 on SuSE Linux Toshikazu Matsuoka (Wed Oct 17 2001 - 01:56:49 PDT)
- Re: Amber6 on SuSE Linux jim caldwell (Wed Oct 17 2001 - 10:00:06 PDT)
distribution of Na+ around DNA Xiaolin Chuang (Wed Oct 17 2001 - 05:04:54 PDT)
image command of ptraj Xiaolin Chuang (Wed Oct 17 2001 - 05:22:20 PDT)
iwrap Xiaolin Chuang (Wed Oct 17 2001 - 05:27:39 PDT)
help seema namboori (Wed Oct 17 2001 - 06:50:53 PDT)
Re: distribution of Na+ around DNA Bill Ross (Wed Oct 17 2001 - 07:32:02 PDT)
Re: possible bug in carnal in AMBER5 Bill Ross (Wed Oct 17 2001 - 14:09:00 PDT)
Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards Ross Walker (Thu Oct 18 2001 - 07:00:48 PDT)
- torsional profile Giulio Rastelli (Thu Oct 18 2001 - 08:29:12 PDT)
- Re: Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards David Konerding (Thu Oct 18 2001 - 08:30:38 PDT)
  - RE: Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards Ross Walker (Thu Oct 18 2001 - 12:29:56 PDT)
  - Interface program installation Sophia Kondratova (Fri Oct 19 2001 - 10:25:19 PDT)
    - Re: Interface program installation David Pearlman (Fri Oct 19 2001 - 14:22:45 PDT)
  - Problem in GIBBS! PRADIPTA Bandyopadhyay (Fri Oct 19 2001 - 13:43:41 PDT)
- RE: Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards DeLano, Warren (Thu Oct 18 2001 - 09:48:53 PDT)
Re: Aqvist LJ parameters Samantha (Thu Oct 18 2001 - 11:34:46 PDT)
Re: generation of small organic molecules on xleap Bill Ross (Sun Oct 21 2001 - 21:48:53 PDT)
xleap: japanese keyboad Toshikazu Matsuoka (Sun Oct 21 2001 - 22:41:02 PDT)
Err in equilibration run A.Madhumalar (Sun Oct 21 2001 - 23:22:09 PDT)
Re: Err in equilibration run Bill Ross (Mon Oct 22 2001 - 00:03:38 PDT)
DNA strands separated... Jithesh P.V. (Mon Oct 22 2001 - 00:07:09 PDT)
question about implicit solvation model with AMBER Howard Feldman (Tue Oct 23 2001 - 07:55:36 PDT)
substracting of MM nonbondeb potential from QM curve Michal Otyepka (Tue Oct 23 2001 - 10:24:44 PDT)
Define flexible residues during MD simulation wentaofu (Tue Oct 23 2001 - 14:59:59 PDT)
- Re: Define flexible residues during MD simulation Bill Ross (Tue Oct 23 2001 - 21:14:35 PDT)
- Methane minimization using Interface Sophia Kondratova (Wed Oct 24 2001 - 07:17:36 PDT)
- param CT-CT-CT-OH Michal Otyepka (Wed Oct 24 2001 - 11:54:56 PDT)
- roar-cp crashed Yuguang Mu (Wed Oct 24 2001 - 14:25:38 PDT)
- how to add Zn Ca parameters Xin Hu (Wed Oct 24 2001 - 16:08:51 PDT)
Re: how to add Zn Ca parameters Bill Ross (Wed Oct 24 2001 - 17:04:58 PDT)
- Re: how to add Zn Ca parameters Eva Darian (Thu Oct 25 2001 - 14:29:50 PDT)
- Need some help with Amber/Linux John Nicholas (Thu Oct 25 2001 - 14:42:52 PDT)
  - Re: Need some help with Amber/Linux David Pearlman (Thu Oct 25 2001 - 18:04:23 PDT)
    - Re: Need some help with Amber/Linux John Nicholas (Fri Oct 26 2001 - 09:19:11 PDT)
NSCM setting to remove center of mass motion Michael G Cooney (Thu Oct 25 2001 - 09:52:09 PDT)
- Re: NSCM setting to remove center of mass motion Sanjeev B.S. (Thu Oct 25 2001 - 20:44:41 PDT)
- unusual parameters pascal bonnet (Fri Oct 26 2001 - 01:06:26 PDT)
Maxwell-Boltzmann distribution of velocities Marcela Madrid (Thu Oct 25 2001 - 12:23:08 PDT)
- Re: Maxwell-Boltzmann distribution of velocities Andreas Svrcek-Seiler (Fri Oct 26 2001 - 03:46:36 PDT)
- Xleap, PDB file format Sophia Kondratova (Fri Oct 26 2001 - 08:00:26 PDT)
  - Re: Xleap, PDB file format Jarrod Smith (Fri Oct 26 2001 - 08:12:49 PDT)
  - Re: Xleap, PDB file format David Case (Fri Oct 26 2001 - 08:59:14 PDT)
  - Re: Xleap, PDB file format Bill Ross (Fri Oct 26 2001 - 09:31:16 PDT)
  - MAX_RSTACK Dr David R V Buckley (Fri Oct 26 2001 - 10:44:02 PDT)
  - RESP charges! PRADIPTA Bandyopadhyay (Fri Oct 26 2001 - 13:24:45 PDT)
belly with GB term Tomoshi Kameda (Thu Oct 25 2001 - 12:54:22 PDT)
Re: (no subject) Bill Ross (Fri Oct 26 2001 - 15:51:36 PDT)
help for restrained minimization xin.hu_at_ndsu.nodak.edu (Fri Oct 26 2001 - 21:10:19 PDT)
- Re: help for restrained minimization Stephane (Mon Oct 29 2001 - 00:39:21 PST)
- Re: help for restrained minimization Bill Ross (Mon Oct 29 2001 - 01:32:16 PST)
- Interface and Sander_classic Sophia Kondratova (Tue Oct 30 2001 - 05:06:03 PST)
  - Re: Interface and Sander_classic David Pearlman (Tue Oct 30 2001 - 10:34:31 PST)
  - IMPORTANT Amber mail list announcement jim caldwell (Tue Oct 30 2001 - 11:44:48 PST)
  - Re: Interface and Sander_classic David Pearlman (Tue Oct 30 2001 - 12:13:42 PST)
- NFFT Hungie Hungie (Tue Oct 30 2001 - 06:43:48 PST)
  - Re: NFFT darden (Tue Oct 30 2001 - 10:03:22 PST)
- How to turn off PME? Hungie Hungie (Tue Oct 30 2001 - 07:49:45 PST)
Err in equilibration run A.Madhumalar (Sun Oct 28 2001 - 02:02:55 PST)
Re: NFFT Michael Crowley (Tue Oct 30 2001 - 08:24:38 PST)
what should change in the parameter? backy_at_ibms.sinica.edu.tw (Wed Oct 31 2001 - 01:52:10 PST)
NPT to NVE ensemble Hungie Hungie (Wed Oct 31 2001 - 05:31:20 PST)
charges for non-standard AAs Uwe Richter (Wed Oct 31 2001 - 05:46:15 PST)
sander_classic wentaofu (Wed Oct 31 2001 - 11:57:07 PST)
- Re: sander_classic Carlos Simmerling (Wed Oct 31 2001 - 12:57:43 PST)

Amber Archive Oct 2001 By Thread