[gmx-developers] Suggestion: move bonded forces in mdrun
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jul 5 17:15:32 CEST 2005
On Wed, 29 Jun 2005, Carsten Kutzner wrote:
>On Wed, 29 Jun 2005, Berk Hess wrote:
>> Do you mean that one could compensate for the larger bonded interaction load
>> by doing less non-bonded interactions on such a cpu?
>Yes, but that is not possible if PME is inbetween.
>> But after looking in the code I was that also PME uses whole molecules,
>> so it is very easy to change indeed.
>Could anybody who has CVS write access do that change or is there
>any reason against it?
Actually I have a tree in which this is implemented, but it is not
completely trivial to get it working with shifts. One does need an extra
coordinate array to do this. In fact the code doesn't work for me yet.
This patch also removes the need for multi-cpu tpr files and
splits all bonded forces over all processors, at the cost of doing
communication of all coordinates and forces over all the processors.
>Dr. Carsten Kutzner
>Max Planck Institute for Biophysical Chemistry
>Theoretical and Computational Biophysics Department
>Am Fassberg 11
>37077 Goettingen, Germany
>Tel. +49-551-2012313, Fax: +49-551-2012302
>eMail ckutzne at gwdg.de
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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://xray.bmc.uu.se/~spoel
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