[gmx-users] Re: mdrun -rerun and box size bug not fixed?
David van der Spoel
spoel at xray.bmc.uu.se
Fri Nov 2 16:24:02 CET 2007
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,
>> 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.
>>> From: "David Mobley" <dmobley at gmail.com>
>>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> To: "Discussion list for GROMACS users" <gmx-users at 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.
>>> Michel Cuendet, Ph.D
>>> Molecular Modeling Group
>>> Swiss Institute of Bioinformatics
>>> CH-1015 Lausanne, Switzerland
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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
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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