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

Justin Lemkul jalemkul at vt.edu
Thu Jan 17 20:07:28 CET 2013

On 1/17/13 2:05 PM, James Starlight wrote:
> Justin,
> so its exacly what  I mean! I dont find any relationship between LJ
> equation in any form and vdw radius of atom. But is it possible to
> modify vdw radius exactly ? E.g I have  united atom as a node which
> vdw must be > 1.5 A. I want to decrease it to 1 A. What should I do
> for it ?

There is no term in any potential energy equation (at least, in the force fields 
used by Gromacs) for an explicitly defined van der Waals radius.



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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