[gmx-users] Graphene topology file

[Justin Lemkul]

On 7/9/14, 9:06 AM, #SUKRITI GUPTA# wrote:
> Thanks for the reply Justin. I just checked my box size again and found it to
> be smaller than the required. Hence I changed the size and ran the simulation
> again. This time energy minimization happened correctly without any change in
> the graphene structure. But when I am doing npt, the water is suddenly moving
> far away from the graphene sheet any tries to agglomerate together causing
> the box size to increase drastically. It is almost like the box is about to
> explode. Its size changes from 2.5A to 11A.
>
> Can you please help me figure out the problem.
>

Does the box expand along z?  Are you using walls?  If not, you should be, in 
the case of pbc = xy.

-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 601
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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