[gmx-users] Re: Simulation of 2D lattice model
jalemkul at vt.edu
Thu Jan 3 13:29:33 CET 2013
On 1/3/13 7:25 AM, James Starlight wrote:
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users