On 9/22/16 1:56 PM, jing liang wrote:
in GROMACS web site there is a recommendation when using CHARMM27 set of
constraints = h-bonds
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rcoulomb = 1.2
DispCorr = no
Is there some issue with the simulations if one uses different values for
Cutoffs are part of the force field. If you start adjusting them, you can throw
things into imbalance and turn the simulation into garbage. With PME, the value
of rcoulomb becomes somewhat irrelevant, though. Verlet will adjust rlist as
needed to buffer the neighbor list, in a manner comparable to what we do in
CHARMM with an explicit vdW cutoff and neighbor list cutoff.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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