Amber Archive Jun 2001: By Thread

Re: sander 6 warming up Andreas Svrcek-Seiler (Fri Jun 01 2001 - 06:53:35 PDT)
sander_classic no mdcrd Daniel Flint (Fri Jun 01 2001 - 07:06:10 PDT)
- Re: sander_classic no mdcrd Christoph Sotriffer (Fri Jun 01 2001 - 06:53:27 PDT)
sander_classic no mdcrd Daniel Flint (Fri Jun 01 2001 - 07:06:10 PDT)
- Re: sander_classic no mdcrd Richard W Dixon (Fri Jun 01 2001 - 08:41:10 PDT)
- Re: sander_classic no mdcrd Richard W Dixon (Fri Jun 01 2001 - 08:41:10 PDT)
ice cube flying through space Marcela Madrid (Fri Jun 01 2001 - 08:10:53 PDT)
- Re: ice cube flying through space Andreas Svrcek-Seiler (Sat Jun 02 2001 - 05:54:55 PDT)
- Adding crystal water using tleap. Sanjeev B.S. (Sun Jun 03 2001 - 08:04:51 PDT)
- compiling amber6 in linux clusters A.Madhumalar (Sun Jun 03 2001 - 09:35:16 PDT)
- How to minimization of Average structure? Xiaolin Chuang (Sun Jun 03 2001 - 09:57:48 PDT)
ice cube flying through space Marcela Madrid (Fri Jun 01 2001 - 08:10:53 PDT)
Re: Adding crystal water using tleap. Bill Ross (Sun Jun 03 2001 - 10:19:32 PDT)
Re: How to minimization of Average structure? Bill Ross (Sun Jun 03 2001 - 11:24:15 PDT)
dsp3 hybrid for P ? Todd J. Minehardt (Sun Jun 03 2001 - 12:47:41 PDT)
90 degree phase offset in AMBER? Kristin Lynne Meagher (Mon Jun 04 2001 - 10:14:27 PDT)
informations Osvaldo A. Santos-Filho (Mon Jun 04 2001 - 13:31:11 PDT)
- Re: informations schayg_at_puskin-a206.sote.hu (Tue Jun 05 2001 - 08:39:03 PDT)
- Error in Gibbs Kian Kani (Tue Jun 05 2001 - 09:42:48 PDT)
- number of atoms for large system Shixiang Yan (Tue Jun 05 2001 - 12:36:50 PDT)
- free energy method Eoin Galligan (Wed Jun 06 2001 - 02:34:53 PDT)
- reflector limitations jim caldwell (Wed Jun 06 2001 - 07:51:05 PDT)
- error msg in leap Eoin Galligan (Wed Jun 06 2001 - 10:30:43 PDT)
  - Re: error msg in leap schayg_at_puskin-a206.sote.hu (Wed Jun 06 2001 - 12:27:49 PDT)
  - LIE method Katherine Wallis Abold (Wed Jun 06 2001 - 14:14:10 PDT)
    - Re: LIE method Wei Wang (Wed Jun 06 2001 - 20:24:26 PDT)
    - leap not reaing torsion from frcmod file Eoin Galligan (Thu Jun 07 2001 - 06:45:22 PDT)
    - AMBER on Hitachi SR8000 Florian Barth (Thu Jun 07 2001 - 13:22:32 PDT)
    - Re: AMBER on Hitachi SR8000 Noriyuki Yamaotsu (Thu Jun 07 2001 - 19:19:09 PDT)
    - error message. Margaret Cheung (Fri Jun 08 2001 - 00:24:07 PDT)
    - Re: error message. Andreas Svrcek-Seiler (Fri Jun 08 2001 - 04:36:41 PDT)
    - a correction, sorry Andreas Svrcek-Seiler (Fri Jun 08 2001 - 06:43:39 PDT)
    - summary of Zn+2 van der Waals radii responses Katherine Wallis Abold (Fri Jun 08 2001 - 07:43:03 PDT)
    - igb=1 error message: Unable to find bonded partner for atom 239 Guanglei Cui (Sat Jun 09 2001 - 13:46:03 PDT)
  - make test.all Elizabeth K. White (Wed Jun 06 2001 - 14:22:46 PDT)
  - 2'-deoxy-uracil Anton B. Guliaev (Wed Jun 06 2001 - 15:36:01 PDT)
benchmark on X-86 Sanjeev B.S. (Tue Jun 05 2001 - 01:23:37 PDT)
Re: AMBER on Hitachi SR8000 Bill Ross (Thu Jun 07 2001 - 14:43:48 PDT)
Zn+2 van der Waals radii Katherine Wallis Abold (Thu Jun 07 2001 - 15:16:14 PDT)
How is the random number used to generate random velocities? Andrew Hoofnagle (Mon Jun 11 2001 - 10:02:37 PDT)
Animating normal modes David Bevan (Mon Jun 11 2001 - 10:36:39 PDT)
atom coordinates Troy Bothwell (Mon Jun 11 2001 - 15:47:59 PDT)
Re: atom coordinates Bill Ross (Mon Jun 11 2001 - 16:29:39 PDT)
Dual-processor performance. Sanjeev B.S. (Mon Jun 11 2001 - 23:45:24 PDT)
Re: Non-standard DNA bases Bill Ross (Tue Jun 12 2001 - 14:39:05 PDT)
Non-standard DNA bases J Suggs (Tue Jun 12 2001 - 16:32:21 PDT)
- Re: Non-standard DNA bases Bill Ross (Tue Jun 12 2001 - 22:29:40 PDT)
  - Re: Non-standard DNA bases David Konerding (Wed Jun 13 2001 - 07:41:09 PDT)
  - GFP chromophore force field parameters Dr Chris L. Brown (Wed Jun 13 2001 - 18:31:56 PDT)
Re: mm_pbsa samantha hughes (Thu Jun 14 2001 - 00:06:47 PDT)
Problem in MD! PRADIPTA Bandyopadhyay (Thu Jun 14 2001 - 10:16:59 PDT)
Is there a potential for speedup in the GB-code ? Andreas Svrcek-Seiler (Fri Jun 15 2001 - 08:05:36 PDT)
coordinate blowup in sander Michael Cooney (Fri Jun 15 2001 - 09:29:05 PDT)
- Re: coordinate blowup in sander jim caldwell (Fri Jun 15 2001 - 10:54:53 PDT)
  - Re: coordinate blowup in sander Carlos Simmerling (Fri Jun 15 2001 - 11:46:36 PDT)
  - An Invitation From The Middle East Chemical Industry iec_at_emirates.net.ae (Sat Jun 16 2001 - 12:34:21 PDT)
  - RESP X GAMESS Dummie Question Jones de Andrade (Mon Jun 18 2001 - 10:22:11 PDT)
  - WHY NOT TRY IT? go5612gwe_at_arabia.com (Mon Jun 18 2001 - 12:02:17 PDT)
  - water parameters+TIP3 water model Satyavani Vemparala (Mon Jun 18 2001 - 13:00:00 PDT)
    - Re: water parameters+TIP3 water model jim caldwell (Tue Jun 19 2001 - 11:52:04 PDT)
    - Linux stability Stephane (Fri Jun 22 2001 - 15:05:29 PDT)
    - (no subject) bxiong (Fri Jun 22 2001 - 19:11:09 PDT)
    - AMBER Phil Cunningham (Tue Jun 19 2001 - 13:53:11 PDT)
    - Re: AMBER jim caldwell (Tue Jun 19 2001 - 15:30:17 PDT)
    - parallel sander Yuguang Mu (Wed Jun 20 2001 - 07:58:39 PDT)
    - Re: parallel sander Sanjeev B.S. (Wed Jun 20 2001 - 10:39:23 PDT)
    - equilibrating water in sander Elizabeth K. White (Wed Jun 20 2001 - 16:00:00 PDT)
    - Re: equilibrating water in sander Yong Duan (Wed Jun 20 2001 - 21:27:02 PDT)
  - PMF calculations Eoin Galligan (Tue Jun 19 2001 - 03:58:26 PDT)
Re: parallel sander Yuguang Mu (Thu Jun 21 2001 - 23:43:07 PDT)
emin after molecular dynamics Nicole Silvester (Fri Jun 22 2001 - 00:41:06 PDT)
gb with explicit water molecules Guanglei Cui (Fri Jun 22 2001 - 09:05:52 PDT)
- PDB old to new Jithesh P.V. (Tue Jun 26 2001 - 23:48:06 PDT)
iwrap & TIP3P model water Xiaolin Chuang (Fri Jun 22 2001 - 09:20:06 PDT)
- Re: iwrap & TIP3P model water Jung-Hsing Lin (Fri Jun 22 2001 - 09:53:00 PDT)
Re: Linux stability Bill Ross (Fri Jun 22 2001 - 13:51:17 PDT)
Re: CCl4 charge problem... jim caldwell (Fri Jun 22 2001 - 14:03:13 PDT)
Re: Wrong compilation artifacts on ES40s? Bill Ross (Sun Jun 24 2001 - 10:59:27 PDT)
- Re: Wrong compilation artifacts on ES40s? Bill Ross (Sun Jun 24 2001 - 12:58:33 PDT)
- Re: Wrong compilation artifacts on ES40s? Sanjeev B.S. (Sun Jun 24 2001 - 13:17:48 PDT)
- AmberFFC version 1.2 Francois Dupradeau (Sun Jun 24 2001 - 13:49:29 PDT)
Wrong compilation artifacts on ES40s? Sanjeev B.S. (Sun Jun 24 2001 - 11:43:11 PDT)
- Re: Wrong compilation artifacts on ES40s? Bill Ross (Sun Jun 24 2001 - 23:51:20 PDT)
- gradual warming + partial solvation Eoin Galligan (Mon Jun 25 2001 - 07:59:44 PDT)
- My input problem in amber6 ! A. Ababou (Mon Jun 25 2001 - 08:54:18 PDT)
- Charges for a 2-iodine-phenol stefania_at_mail.unimo.it (Mon Jun 25 2001 - 09:29:27 PDT)
- Machine file for sgi kian kani (Mon Jun 25 2001 - 10:25:21 PDT)
- Best Topolgy for Linux Cluster Sanjeev B.S. (Tue Jun 26 2001 - 05:17:51 PDT)
- Energy calculation Prem Raj Joseph (Tue Jun 26 2001 - 09:34:38 PDT)
- begginer's question about RESP and GAMESS Jones de Andrade (Tue Jun 26 2001 - 10:44:02 PDT)
Re: begginer's question. jim caldwell (Tue Jun 26 2001 - 12:20:32 PDT)
Resp input confusion. jim caldwell (Tue Jun 26 2001 - 14:55:07 PDT)
RE: CCl4 charge problem... Thomas.Fox_at_bc.boehringer-ingelheim.com (Wed Jun 27 2001 - 01:16:19 PDT)
RE: CCl4 charge problem... (part II) Thomas.Fox_at_bc.boehringer-ingelheim.com (Wed Jun 27 2001 - 03:04:17 PDT)
tleap input format A.Madhumalar (Wed Jun 27 2001 - 06:20:02 PDT)
AMBER on mpi Marco Punta (Wed Jun 27 2001 - 10:39:46 PDT)
resp charges: ccl4 jag vs. g98 jim caldwell (Wed Jun 27 2001 - 15:51:49 PDT)
Parameter for abasic nucleotide Numan Oezguen (Wed Jun 27 2001 - 19:48:58 PDT)
re: Amber compiling on Alpha Clusters Redhat Linux Chuck Schneider (Thu Jun 28 2001 - 05:08:41 PDT)
folding simulations Elizabeth K. White (Thu Jun 28 2001 - 14:52:19 PDT)
- Re: folding simulations David Case (Thu Jun 28 2001 - 17:27:00 PDT)
- Problems with AMBER John Finke (Thu Jun 28 2001 - 18:04:52 PDT)
Re: Problems with AMBER Bill Ross (Thu Jun 28 2001 - 19:49:52 PDT)
- Re: Problems with AMBER Bill Ross (Thu Jun 28 2001 - 19:49:52 PDT)
- Re: Problems with AMBER John Finke (Fri Jun 29 2001 - 15:55:06 PDT)
- Re: Problems with AMBER Bill Ross (Fri Jun 29 2001 - 16:23:06 PDT)
TIP3P Guanglei Cui (Thu Jun 28 2001 - 22:22:57 PDT)
torsion parameters needed Guanglei Cui (Thu Jun 28 2001 - 22:40:06 PDT)
Re: TIP3P Bill Ross (Thu Jun 28 2001 - 23:34:47 PDT)
AMBER parameter database Dr Richard Bryce (Fri Jun 29 2001 - 09:47:18 PDT)

Amber Archive Jun 2001 By Thread