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

Justin Lemkul jalemkul at vt.edu
Wed Jan 2 16:17:21 CET 2013

On 1/2/13 10:14 AM, Bogdan Costescu wrote:
> 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.

One must use the right atom type (for LJ purposes) in conjunction with correct 
bonded parameters.  You can create whatever monster atom you choose with any 
arbitrary valence, as long as you create the right bonded parameters that govern 
its geometry.  Since MD simulations don't explicitly consider valence, you can 
do whatever you want, in theory.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list