[gmx-users] Regarding Position restraint and freezegroups

rahul seth rahul.seth.gromacs at gmail.com
Thu Aug 29 23:24:36 CEST 2013

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
pressure coupling, other particles around the frozen group can have their
positions scaled and thus collide with the frozen group, which has remained
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?

On Thu, Aug 29, 2013 at 4:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 8/29/13 3:25 PM, rahul seth wrote:
>> Hello,
>> I have been performing simulations with nanotubes. I read several entries
>> in the gromacs users forum regarding the correctness of the usage of the
>> freeze groups in simulations.
>> However, I am trying to perform NPT simulations at two different
>> temperatures using berendsen and parrinello-rahman barostat respectively
>> freezing the carbon nanotubes and position restraining them at the same
>> time.
> Why would this be necessary?  Both position restraints and freezegrps
> restrict movement; under what circumstances are both necessary?  Hopefully,
> from a very recent thread on this topic, it should be abundantly clear that
> the combination of pressure coupling and frozen atoms is fundamentally
> unsound.
>  I am using refcoord-scaling = com
>> I do not have any information regarding the bonded interactions of the
>> carbon nanotubes since I am freezing and position restraining them
>> anyways.
> Why not?  CNT simulations are not novel; plenty of people have used
> reasonable parameters for bonded and nonbonded interactions.
>  Interestingly, although Berendsen barostat keeps the diameter constant at
>> a
>> fixed value the parrinello-rahman barostat changes the diameter of the
>> nanotube quite significantly at the higher temperatures. Can anyone
>> explain
>> what is going on?
> The Parrinello-Rahman barostat allows for wider oscillations in the
> pressure, and higher temperatures exacerbate the outcome.  I suspect that
> the combination of a non-physical restraint/frozen combination and the
> natural behavior of the barostat causes artifacts like this.
> -Justin
> --
> ==============================**====================
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
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> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
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