[gmx-users] Graphene topology file

[abhijit Kayal]

Hi Sukriti,
 Copy the oplsaa.ff directory to your working directory. Then in
ffnonbonded.itp file add the following lines..
 opls_995   C      6    12.01100     0.000       A    3.40000e-01
3.61200e-01
 opls_996   C      6    12.01100     0.000       A    3.40000e-01
3.61200e-01
 opls_997   C      6    12.01100     0.000       A    3.40000e-01
3.61200e-01

Then in   atomname2type.n2t file add the following lines.
C    opls_995    0      12.011  2    C  0.142  C 0.142
C    opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142
C    opls_997    0      12.011  1    C  0.142

Then use g_x2top. This will work.

Thanks
 Abhijit


On Thu, Jul 3, 2014 at 3:11 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
wrote:

> 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 The tutorial is indeed outdated but the logic is fairly sound.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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-- 
Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur