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

Justin Lemkul jalemkul at vt.edu
Thu Jan 3 18:11:25 CET 2013

On 1/3/13 11:49 AM, James Starlight wrote:
> Justin,
> 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.

I'm assuming you've simply switched the atom types here.  A CH2 should not have 
3 other bonds.

> 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 ?

You can do anything you like, but you'd better have good justification for it. 
Making ad hoc changes to force fields that were not necessarily designed to do 
what you think it should is generally very unwise.  Whatever you do, make 
changes in a local copy of the force field so you don't screw up other 
simulations later on, or even better, make a special [atomtypes] directive in 
your .top file.

> How I could prevent rotation of the lattice as the whole object ? (
> simulation in vacuum in NVT) without any posres ?

I can't think of a way to do this, nor would it have any real functional 
purpose.  You can remove rotation and translation afterwards with trjconv.

> 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)

If you're running in vacuo, you should turn off PBC and use infinite cutoffs, 
otherwise you likely will have periodicity artifacts and you are not truly 
simulating in vacuo.

> 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/ ) ?

Some boxes have hexagonal cross-sections (see the manual) that might be useful. 
  In a basic sense, all you need to have is atoms that should be bonded to one 
another through a periodic boundary should be separated by one bond length (i.e. 
half a bond length on either side of the box) and make sure these bonds are 
added to the topology (probably by hand).  Then the periodic_molecules option 
works its magic and you have an infinite lattice.



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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