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

[fantasticqhl]

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!
>
>
>
>