[gmx-users] Graphene modeling

Justin Lemkul jalemkul at vt.edu
Mon May 15 14:15:21 CEST 2017

On 5/14/17 9:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Hi GROMACS users,
> I want to model a graphene sheet. I used the instruction stated in link http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube. I put the cnt_oplsaa.ff folder in the directory where I want to run the rest of the work. Also, I rename the residues of the graphene to “CJ” and the atoms to “C”. but, when I want to use “gmx x2top”, I get the error that says it cannot find any forcefield type for the atoms. Can you please help me to figure this out?

Since all you have are C atoms, this should require only a one-line .n2t file 
(or addition to an existing one) that specifies the proper equilibrium bond 
length for C-C in your structure.  Without seeing your .n2t file and the x2top 
screen output, there's nothing to suggest other than your .n2t file is somehow 
inadequate for what you're trying to do.



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


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