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

Justin Lemkul jalemkul at vt.edu
Thu Jan 3 13:29:33 CET 2013

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


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