[gmx-users] how to maintain planarity of graphene sheet

[Justin Lemkul]

On 1/14/16 2:13 AM, jagannath mondal wrote:
> Hi
>
>    Which restraints can one  use to maintain planarity of graphene sheets
> while performing MD simulations of their association ? I guess
> flat-bottommed restraints will not work.
>

Planarity is governed by dihedrals, either proper, improper, or both, depending 
on the form of the force field.  If your simulations conditions lead to 
deformation, either the force field representation is wrong or whatever you're 
doing during the simulation is not physically sound.  Though, AFAIK graphene is 
not completely planar; some out-of-plane distortions are to be expected, as with 
any aromatic system.  The amplitude of that distortion is generally not large 
but is dependent upon whatever is going on in the simulation.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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