[gmx-users] Re: mdrun -rerun and box size bug not fixed?
michel.cuendet at isb-sib.ch
Fri Nov 2 14:51:09 CET 2007
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.
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
>>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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