[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

Dr. Vitaly Chaban vvchaban at gmail.com
Sat Apr 6 18:07:10 CEST 2013

In systems of such kind, everything will depend on the atom of the ligand,
which coordinated by copper ion.

Perform ab initio geometry optimization and find the optimal distance. Then
adjust sigma(s).

Dr. Vitaly Chaban

There is a copper ion with four ligands in my system. I am going to
> study this system using MD simulations.
> For the vdW parameters, R*=1.74 angstrom and epsilon=1.14 kcal.mol from
> one paper will be used in our
> simulations. I already found the parameters of copper ion (Cu2+) in the
> OPLS-AA/L force field files:
> sigma= 2.08470e-01, epsilon=4.76976e+00, which are for Cu2+ without
> ligands. The two epsilon are the same,
> just with different units.
> My question is that I do not know how to convert the vdW radius to
> sigma. I found that the vdw radius of copper is
> 1.4 angstrom, and the sigma in the force field file is 2.08470e-01.
> Could someone tell me how to do the converting?
> Thanks very much!

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