[gmx-users] PME and atom-based cutoffs
spoel at xray.bmc.uu.se
Wed Dec 10 08:35:03 CET 2003
On Wed, 2003-12-10 at 02:12, Malcolm Gillies wrote:
> Are atom-based cutoffs (rather than group based) used automatically when
> coulombtype = PME ?
No! We still use charge groups with PME, mainly for efficiency of
neighborsearching. It does not make a difference in energy and forces,
> I want to make sure that I can dispense with defining proper charge
> groups for my custom residue types, if I only plan to use PME.
That shouldn't be a problem indeed, just make them not too big (3-4
atoms). The charge groups also influence the Van der Waals forces in the
same manner, but if your cut-off is "large enough"(TM) that shouldn't be
a problem either.
> Malcolm Gillies <Malcolm.B.Gillies at anu.edu.au>
> Postdoctoral Fellow, Computational Proteomics and Therapy Design Group,
> John Curtin School of Medical Research, Australian National University
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David van der Spoel, PhD, Assist. 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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