[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L
fantasticqhl
fantasticqhl at gmail.com
Mon Apr 8 15:36:13 CEST 2013
Dear Dr. Vitaly Chaban,
Thanks very much for your patient explanation. Yeah, you are right, that
is what I want to know: how you tuned this parameter?
Since then, if I want to set a new atom type and I know its vdw radius,
so how should I set the sigma for it based on the vdw radius,
which should be in agreement with OPLS-AA/L force filed? Could you give
me some suggestions?
I guess that I have to tune it by myself this time, right? Thanks in
advance!
All the best,
Qinghua Liao
On 04/08/2013 03:21 PM, Dr. Vitaly Chaban wrote:
> 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
> <mailto: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 <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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