[gmx-users] freezegrps changing coordinates in NPT simulations

Justin Lemkul jalemkul at vt.edu
Fri May 15 03:31:22 CEST 2015

On 5/14/15 1:57 PM, jwillcox at andrew.cmu.edu wrote:
> Hello again,
> I'm running a simulation with graphene as a periodic molecule.  I've
> frozen the carbons in place in the mdp file using:
> freezegrps               =  CG_CE
> freezedim                = Y Y Y
> but when I run an NPT simulation, the entire system shrinks (including
> moving the carbons closer together) until it crashes.  Everything works
> fine for NVT and minimization.
> Are there any tricks to freezing groups in NPT simulations?

Freezing and pressure coupling aren't compatible.  See cautionary notes in the 
manual about this case.



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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