[gmx-users] Regarding Position restraint and freezegroups

Justin Lemkul jalemkul at vt.edu
Thu Aug 29 23:29:41 CEST 2013

On 8/29/13 5:24 PM, rahul seth wrote:
> Thanks. I followed that post on gromacs. In one of the posts you have
> particularly written:
> "The refcoord-scaling option doesn't matter with frozen groups.  Anything
> that is
> frozen, by definition, never has its position updated.  Under the influence
> of
> pressure coupling, other particles around the frozen group can have their
> positions scaled and thus collide with the frozen group, which has remained
> in
> its original location."
> I think I am observing something different in this case. I froze the CNTs
> in my case, and the frozen groups infact were scaled with the boxes. To
> nullify such effects, I had used position restraints. It worked perfectly
> for berendsen barostat and my question is why is it not happening with
> parrinello-rahman barostat.
> Is there a way to know for sure that this is indeed something caused by the
> nature of the barostat?

Test with either freezegrps or restraints, but not both.

The combination of pressure coupling + position restraints + freezegrps has 
probably never been tested (because it shouldn't be used!) and thus it is 
entirely possible that you're seeing buggy behavior.  It wouldn't be a bug worth 
fixing, because the combination doesn't make physical sense.  It sounds like the 
restraints and the freezing are fighting one another under one condition, but 
not another.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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