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

[Dr. Vitaly Chaban]

Dear Qinghua Liao -

In that case, I am just wishing you luck with the copper containing systems.

Are you going to simulate copper-ligand interactions using Coulomb+LJ
potential only? I would guess it is a chemical bonding case. Maybe the
Morse potential (additionally) can be of better service?


Dr. Vitaly Chaban




On Mon, Apr 8, 2013 at 1:09 PM, fantasticqhl <fantasticqhl at gmail.com> wrote:

>  Dear Dr. Vitaly Chaban,
>
> Thanks very much for your explanation. I guess that I get what you mean
> now! Thanks!
>
> All the best,
> Qinghua Liao
>
> On 04/07/2013 11:35 AM, Dr. Vitaly Chaban wrote:
>
> The equation is a direct consequence of LJ-12-6 equation. This equation is
> used in OPLS and most other force fields.
>
>  The difference you found originate from the fact that, besides LJ
> potential, there is much stronger Coulomb potential in the copper-ion case.
> If you run simulations, you will see that copper-ligand distance is smaller
> than the sum of their sigmas multiplied by pow (2, 1/6).
>
>
>  Dr. Vitaly Chaban
>
>
>
>
>
>
>  On Sun, Apr 7, 2013 at 11:28 AM, fantasticqhl <fantasticqhl at gmail.com>wrote:
>
>>  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>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!
>>>>>
>>>>>
>>>>>
>>>
>>
>>
>
>