[gmx-users] How to modify the rtp file for graphene?

[Justin Lemkul]

On 7/31/14, 10:26 PM, Andy Chao wrote:
> Dear GROMACS Users:
>
> I would like to simulate the graphene-electrode based electric double layer
> capacitor device.  I need to convert the .gro file to .top file by using
> the g_x2top command.  The command that I used is the following:
>
> g_x2top -f device1.gro -ff oplsaa -o device1.top
>
>
> My question is, how to modify the .rtp file for graphene carbon atom on the
> electrode?
>

You don't.  Only pdb2gmx uses .rtp files and they are generally for linear 
polymers (with limited exceptions handled by specbond.dat).  g_x2top uses .n2t 
files, and given the uniform nature of graphene bonding, creating a suitable 
.n2t file is trivial; see documentation in the manual and online.

-Justin

> In other words,
>
> [ c4]
> [ atoms ]
> ..
> [ bonds ]
>
> [ dihedrals ]
> ...
>
> [impropers ]
> ...
>
>
> Thanks!
>
> Andy
>

-- 
==================================================

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

==================================================