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
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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