[gmx-users] Graphene topology file

[Justin Lemkul]

On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote:
> Dear all,
>
>
> I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial.
>
> http://chembytes.wikidot.com/grocnt
>
>
> But I think this tutorial is quite old and hence suitable for older version of gromacs as it still uses FF.dat file. Moreover if i am trying to make a new forcefield directory with name graphite_oplsaa containing the modified files like .n2t,.rtp and .itp, its giving me an error that "Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path". When I try to add this forcefield in original path ie. user/share/gromacs/top, it does not allow me to do that as i am not the administrator. Can anyone please let me know how to create the topology file. I require 3 graphene sheets with pbc. I have created the .pdb file using nanobuilder in vmd.
>

The tutorial is indeed outdated but the logic is fairly sound.  You don't have 
to modify anything in $GMXLIB (system-wide); you can just create an .n2t file in 
the working directory and it will override the one at the force field level.

-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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