[gmx-users] Regarding Position restraint and freezegroups

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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