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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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