[gmx-users] Graphene topology file

[Dr. Vitaly Chaban]

Graphene topology is like for tube, so

C .... C
C ... C ... C
C .... C  ....C  .... C

to the N2T file and you are done.


Dr. Vitaly V. Chaban


On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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 The tutorial is indeed outdated but the logic is fairly sound.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
>
> --
> ==================================================
>
> 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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