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

Leandro Bortot leandro.obt at gmail.com
Sun Dec 30 07:41:47 CET 2012

Hi Starlight,

     I had an idea right now... Maybe if you freeze every atom of your
system only in one dimension you will get a good approximation of a 2D
system. Of course you would need to make the coordinates accordingly, e.g.
placing the system in the x-y plane and freezing the z dimension. I never
tried this, it is just an idea but if you are stuck it may be worth trying.

     You can certainly make the topology and/or coordinates by hand. Maybe
you will have to use many impropers in order to keep everything 2D. I
suppose you can start from the forcefield files for the sidechains of TRP,
HIS and PHE, which are planar. Anyway I don't have much experience in
manual construction of topologies so I think others can give you more
helpful and specific advice in this regard.
     Additionally... by the image you sent this system does not seem to be
2D. It looks like several cyclohexanes bonded to each other while it should
look like several benzenes.

I hope it helps,

2012/12/28 James Starlight <jmsstarlight at gmail.com>

> By the way is it possible to make such topology simple by hands (in
> any all atom ff like charmm)?
> E.g I have simple 2D latice
> (http://imageshack.us/photo/my-images/543/lattice.png/ )
> So I want to obtain topology in which bonds, angles and impropers
> would be defined (assumming that all dihedrals are frozen).
> James
> 2012/12/27, James Starlight <jmsstarlight at gmail.com>:
> > Dear Gromacs Users!
> >
> >
> > I want to simulate simple 2D lattice model consisted of arbitrary
> > atoms connected by single bonds. Have somebody else tried to do such
> > simulations ? I'll be very thankful for useful template of topology as
> > well as coordinates.
> >
> > James
> >
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