Michel Cuendet wrote:
Dear David and Berk,
I am investigating further to understand why I don't get the same
energies with -rerun. I will report next week.
if you are using xtc files you will never get the same energies as in
the original run because of the reduced precision in these files.
Thanks for your replies,
Michel
I just checked the 3.3.1 source code in md.c and the box is copied
from the xtc file.
I don't know where your problems could come from.
Berk.
From: "David Mobley" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Subject: Re: [gmx-users] mdrun -rerun and box size bug not fixed?
Date: Thu, 1 Nov 2007 06:12:56 -0700
Dear Michel,
Are you sure you're using 3.3.1? I have not checked this specific
issue -- but I have checked that if I run hydration free energy
calculations in patched 3.3.0, and again in patched 3.3.1, and do my
usual free energy analysis using mdrun -rerun, I get the same values.
That either tells me that (a) the patch is in 3.3.1 also, or possibly
(b) that the problem is small enough for hydration free energies that
I'm missing it.
Anyway, hopefully (a) is true, otherwise I'm going to need to repeat a
LOT of work (and be very grumpy). Keep me posted on this.
Thanks,
David
==========================================================
Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland
www.isb-sib.ch/groups/Molecular_Modeling.htm
==========================================================
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
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