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

[fantasticqhl]

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!
>>
>>