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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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