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

Justin Lemkul jalemkul at vt.edu
Wed Jan 2 16:09:56 CET 2013

On 1/2/13 8:58 AM, James Starlight wrote:
> Bogdan,
> Thank you for explanation. Indeed the problem was in the LINCS
> constrains which was not required for the lattice system.
> 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 ?

The valence of an atom is whatever you assign it in the topology.  Carbon atoms 
can be planar, as in aromatic rings of amino acids, without any issue.



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


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