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

[Justin Lemkul]

On 1/3/13 7:25 AM, James Starlight wrote:
> Justin,
>
> yes, the main task is the parametrization of the simple 2D lattice
> which I created from sp3 carbons as the nodes. Now the main task is
> the reducing of that model  to simplest 2D lattice made from 1 type of
> any atom connected with the 3 adjacent nodes via flexible bonds.
>
> Might I define new atom type for that node   in the atomname2type.n2t
> file placed to the work dir or should I add that atom to the ffbonded
> of the opls or gromos ff ?
>

You can't define atomtypes in .n2t files; they can only make use of existing 
types.  You need to modify ffnonbonded.itp, not ffbonded.itp in that case.  I 
still don't see why you would need a new type; this would only be required to 
introduce new LJ parameters.  You can use existing united-atom types and define 
as many bonds to them as you want (regardless of whether or not they make 
chemical sense) in the .n2t file.

-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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