[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time)

[Bogdan Costescu]

On Mon, Mar 23, 2015 at 5:33 AM, Alex <nedomacho at gmail.com> wrote:

>  I specifically want to reparameterize the bond, angle, and the dihedral
> constants with something that I know to be at least somewhat representative
> of graphene and isn't something from oplsaa, which comes from an entirely
> different paradigm.
>

I was in your situation about some years ago and couldn't find any way
around generating topologies on my own, without using the GROMACS tools. As
you could already see most GROMACS tools are not suitable for graphene/CNT
type of systems. Topologies are well documented and you gain enormously in
flexibility by tailoring the process to your needs.

Good luck,
Bogdan