From owner-chemistry:~at~:ccl.net Fri Sep 14 12:46:01 2007
From: "Rick Venable venabler-$-nhlbi.nih.gov" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL: simulation
Message-Id: <-35154-070914124429-17189-9Tyl6CneRRwjmCU0Pp8z3w.:.server.ccl.net>
X-Original-From: Rick Venable <venabler()nhlbi.nih.gov>
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Date: Fri, 14 Sep 2007 12:11:07 -0400
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Sent to CCL by: Rick Venable [venabler]*[nhlbi.nih.gov]
Procedural details tend to be somewhat specific to the program being being
used.  Major academic simulations packages such as AMBER, CHARMM, GROMOS or
GROMACS, and NAMD each have their own respective web sites and/or mailing
lists for questions of this nature.

AMBER   amber.scripps.edu
CHARMM  www.charmm.org
GROMOS  www.igc.ethz.ch/gromos/
GROMACS www.gromacs.org
NAMD    www.ks.uiuc.edu/Research/namd/

-- 
Rick Venable     5635 FL/T906
Membrane Biophysics Section
NIH/NHLBI Lab. of Computational Biology
Bethesda, MD  20892-9314   U.S.A.
(301) 496-1905   venabler AT nhlbi*nih*gov


On 9/14/07 8:01 AM, "Nahren Mascarenhas meetnahren,yahoo.com"
<owner-chemistry:+:ccl.net> wrote:

> 
> Sent to CCL by: "Nahren  Mascarenhas" [meetnahren-#-yahoo.com]
> Dear CCL Members,
> 
> I have just started to work on simulation studies.
> I want to know the exact procedure for performing the same.
> I have used the following:
> 1000 steps of Steepest Descent Minimization
> 1000 steps equiliberation at 300 K
> followed by 150 ps simulation
> 
> 
> your advise and suggestions will help me a lot
> 
> nahren>