[gmx-users] Re: Simulation of 2D lattice model

[Bogdan Costescu]

On Wed, Jan 2, 2013 at 2:58 PM, James Starlight <jmsstarlight at gmail.com> wrote:
> By the way now I'd like to simulate the same 2D flexible ( in non
> planar hybridization) lattice but consist of non-hydrogens atoms only
> ( only atoms forming lattice scaffold ). Does it possible to change
> Carbon atom-valence (from 4 to 3) preventing tetragonal-like geometry
> ( >c- ) or should I use anothe atom type for such lattice ?

I can't imagine how it can be both "non planar hybridization" and
"preventing tetragonal-like geometry", but maybe I don't understand
your intentions. Assuming you do want a change in geometry - from
tetragonal to planar - then you need to use different parameters to
describe the different geometry, it's not only about changing valence.
If you use OPLS-AA, this means a change of atom type from something
like C sp3 (f.e. opls_139) to sp2 (f.e. opls_147) - both these types
chosen for having zero charge.

Cheers,
Bogdan