[gmx-users] NPT with implicit solvent
jalemkul at vt.edu
Wed Sep 23 15:35:36 CEST 2015
On 9/23/15 4:18 AM, Sana Saeed wrote:
> hi gmx users,i am running an implicit solvent simulation and i get error with NPT. i checked different tutorials and no one used NPT with implicit solvent. may i know the reason of why not using equilibration with implicit. thanks in advance.
Because it doesn't make sense. You'd need a periodic cell, which would just
collapse down to the size of your solute, and you'd end up simulating a
pseudo-crystalline system (also triggering a fatal error related to the box size
and your cutoffs, which is probably the one you're getting).
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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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