[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L
fantasticqhl
fantasticqhl at gmail.com
Sun Apr 7 11:28:55 CEST 2013
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 <fantasticqhl at gmail.com
> <mailto:fantasticqhl at 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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