Dear Dr. Vitaly Chaban,
Thanks very much for your reply. My question is the relationship between
van der Waals radius and sigma in the OPLS-AA/L force filed files of
Gromacs.
Of course I did ab initio optimizations of my system, but I do not know
there is some relation between the optimal bond length (copper--atom of
the ligand) and sigma.
Could you please be more clear and give a little detailed explanation?
Thanks very much!
All the best,
Qinghua
On 04/06/2013 06:07 PM, Dr. Vitaly Chaban wrote:
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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