[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L
Dr. Vitaly Chaban
vvchaban at gmail.com
Mon Apr 8 15:21:33 CEST 2013
I think your misunderstanding comes from the belief that sigma (as they are
tabulated in the force field files) should *exactly correspond* to the VDW
diameter, as in encyclopedia.
This is simply not the case. In reality, sigmas in the force fields are
"tuned" in order to give right interatomic distances AFTER you turn on all
the necessary potentials (Coulombic attraction in case of OPLS).
Dr. Vitaly Chaban
On Mon, Apr 8, 2013 at 3:14 PM, fantasticqhl <fantasticqhl at gmail.com> wrote:
> 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>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!
>>>>>>
>>>>>>
>>>>>>
>>>>
>>>
>>>
>>
>>
>
>
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