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

[Dr. Vitaly Chaban]

On Tue, Apr 9, 2013 at 9:39 AM, fantasticqhl <fantasticqhl at gmail.com> wrote:

>  Dear Dr. Vitaly Chaban,
>
> Thanks very much for your patient and detailed suggestions on this
> problem. Actually, I am doing what your suggested now.
> I optimized the copper-ligand complex using QM method, and then did some
> QM scannings to derive the bond and angle force constants.
> Right now, I am doing the MM scanning using the same coordinates which
> were used in the QM scanning. What we want is that the MM curves
> can reproduce the QM curves.
>


I think it is simply impossible in your case to reproduce the QM curves.
You neglect charge transfer from copper to the ligand, resulting a chemical
bond formation, you neglect finite T effect in your MD. If you want to
remain in the framework of LJ+Coulomb, the best think you can get is
reproduction of ion-ligand binding energy and more or less adequate
distance ion-closest atom of the ligand




> But some of them agreed well, some of them did not. So I try to tune the
> sigma of the liganded atoms, however,
> it is a little complicated to tune many liganded atoms at the same time. I
> am still trying to work it out.
>
>

Start from the sigma for "ion-closest atom of the ligand". All other atoms
will adjust automatically, since they are connected all together within the
ligand.

My personal viewpoint, which you may share or not, is not to do anything
with sigmas of other atoms of the ligand. It is best for future portability
to limit refinement to the ion only.




>  It seems that you have much experience on such problems, could you please
> give me some suggestions on tuning the sigmas of atoms again?
> Thanks very much in advance!
>
>
> All the best,
> Qinghua Liao
>
>
>
> On 04/08/2013 03:51 PM, Dr. Vitaly Chaban wrote:
>
>
>  On Mon, Apr 8, 2013 at 3:36 PM, fantasticqhl <fantasticqhl at gmail.com>wrote:
>
>>  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,
>>
>
>
>  You cannot set the sigma based ONLY 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!
>>
>
>
>  I would do the following:
>
>  1) Optimize ion-ligand complex using ab initio. Write down binding
> energy and optimal distance;
> 2) Construct topology for classical MD using approximate sigma;
> 3) Calculate energy and distance from classical MD;
> 4) Compare them to distance and energy from ab initio;
>  5) If you are not satisfied, adjust your sigma;
> 6) Repeat classical MD until the difference between ion-ligand distance in
> classical MD becomes reasonably similar to that in ab initio.
>
>  To preserve compatibility with OPLS, use the same level of theory in ab
> initio, which they used when derived OPLS. Keep in mind that their original
> level of theory is not so perfect...
>
>
>  Dr. Vitaly Chaban
>
>
>
>>
>> All the best,
>> Qinghua Liao
>>
>>
>>
>>
>>
>