[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L
fantasticqhl
fantasticqhl at gmail.com
Mon Apr 8 15:14:45 CEST 2013
Dear Dr. Vitaly Chaban,
Thanks very much for concern on my research! We are going to the use the
bonded model together with Coulomb and LJ potentials.
My problem is that vdw radius and its sigma do not follow the equation
of Rvdw = pow(2, 1/6)*sigma in the OPLS force field files,
not just for copper. That's why I sent these e-mails for suggestions. I
am sorry for the unclear.
All the best,
Qinghua Liao
On 04/08/2013 01:22 PM, Dr. Vitaly Chaban wrote:
> 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
> <mailto: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 <mailto: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 <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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