[gmx-users] Graphene topology file

Justin Lemkul jalemkul at vt.edu
Mon Jul 7 12:41:46 CEST 2014

On 7/7/14, 12:36 AM, #SUKRITI GUPTA# wrote:
> Hi all,
> After getting the topology file for graphene, when i tried to freeze graphene
> and do energy minimization with just water molecules around it, then the
> graphene structure becomes distorted ie. the upper layer of the graphene
> shifts down and the terminal carbons forms bond with each other. I think this
> happens because i did not add terminal hydrogens to the graphene sheet as I
> wanted periodic boundary conditions in x y direction. Also the box size in z
> direction is shown to be zero in the output file of energy minimization. Can
> anyone please let me know how to solve this problem?

If the z-dimension is zero, then your box isn't set up properly.  Likely you're 
just getting clashes between periodic images.  Setting up a proper box should 
solve the problem.



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


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