[gmx-users] NPT with implicit solvent

Justin Lemkul 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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