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

[David van der Spoel]

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.
________________________________________________________________________
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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