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

James Starlight jmsstarlight at gmail.com
Thu Jan 3 17:49:18 CET 2013


I've made new lattice model in GROMOS united atoms. I've used 2 nodes
- CH2 (ca) for atom with 3 bonds as well as CH1 (CB) for boundary
atoms with 2 bonds to adjacent nodes.
That system is considerably rigid in comparison to the lattice which
I've simulated in OPLS all atom ff.

Does it possible to change VDW(LJ) parameters for both nodes in the
top file or should I modify existing atom types in ffnonbonded ?

How I could prevent rotation of the lattice as the whole object ? (
simulation in vacuum in NVT) without any posres ?
Its not possible to use very small box dimensions due to the rvdv= 1.4
in gromos ff
(if I define box vectors compatible with the size of the lattice I've
obtain error in grompp)

Also in connection to the above question with the box size I also
wounder like to know how I could use ; periodic_molecules  options
with such lattice which asymmetric on left and right boundaries (
picture http://imageshack.us/photo/my-images/543/lattice.png/ ) ?

Thanks for help


2013/1/3, Justin Lemkul <jalemkul at vt.edu>:
> 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
> --
> ========================================
> 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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