[gmx-users] how to exclude some atoms from coulomb interaction calculation?

David van der Spoel spoel at xray.bmc.uu.se
Fri Sep 8 11:02:52 CEST 2006

Cherry Y. Yates wrote:
> Dear all,
> I did a massive MD simulation of nanostructure. In my calculation, over 
> 80% atoms have zero charge and the main CPU time is devoted to Coulomb 
> interaction. I wonder if anyone knows how to exclude these neutral atoms 
> from Coublomb interaction so that a lot of CPU time will be saved.
They are excluded already. GROMACS does not compute nonbonded 
interactions when the result is zero. This can be due to charges or LJ 
parameters being zero.

> Many thanks,
> Cherry
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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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