On 9/22/16 1:56 PM, jing liang wrote:
Hi, in GROMACS web site there is a recommendation when using CHARMM27 set of parameters: 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 cutoff distances?
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 -- ================================================== 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 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
