Dear Dr. Vitaly Chaban,

Thanks for the explanation. I know this equation. However, the van der Waals radius and its counterpart sigma in OPLS-AA/L force field files do not follow this equation.

For example, the vdw radius of copper ion is 1.4 angstrom, and its sigma is 2.08470e-01 (I guess the unit is nm). pow(2, 1/6) is more than 1, so obviously this equation does not work with copper. So do other atoms. I guess that there might be an additional coefficient for this equation in gromacs. That's the purpose for asking. Thanks very much!


All the best,
Qinghua

On 04/07/2013 10:48 AM, Dr. Vitaly Chaban wrote:
Dear Qinghua -

The formal relation is diameter = pow (2, 1/6) * sigma, provided that you have only LJ potential in your interacting subsystem.

If this is not the case, an optimal sigma can only be found iteratively.


Dr. Vitaly Chaban





On Sun, Apr 7, 2013 at 10:36 AM, fantasticqhl <fantastic...@gmail.com <mailto:fantastic...@gmail.com>> wrote:

    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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