A B wrote:
Please refer to my recent paper, J. Chem. Theor. Comp. 2 (2006) 1-11.
Yes, this is exactly what I mean - an appropriate smoothing function
("shift") works fine, but simple group-based truncation does not; that
this does not work has indeed been known since long before GROMACS was
born. Maybe the "NVE cutoff" issue is merely semantic, where cutoff
should be interpreted in a slightly restricted sense as "spherical
cutoff method using group-based truncation"?
You should use neither, at least not for Coulomb. Only PME can be used
for systems containing charges. For system containing exclusively
neutral molecules, you can use a shift function, if the cut-off is
longer than the range of the interaction. For water that would be
roughly 1.2 nm.
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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
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