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

fantasticqhl fantasticqhl at gmail.com
Sat Apr 6 16:35:39 CEST 2013

Dear GMX users,

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!

All the best,

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