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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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