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

[fantasticqhl]

Dear Dr. Vitaly Chaban,

Thanks very much for your explanation. I will try to use the method as 
you suggested to do the validation. Thanks!

All the best,
Qinghua Liao


On 04/09/2013 12:10 PM, Dr. Vitaly Chaban wrote:
>
>
>
> On Tue, Apr 9, 2013 at 11:03 AM, fantasticqhl <fantasticqhl at gmail.com 
> <mailto:fantasticqhl at gmail.com>> wrote:
>
>     Dear Dr. Vitaly Chaban,
>
>     Thanks very much again. I am sorry for the unclear, charge
>     transfer was also taken into account for the complex, I did not
>     mentioned in the last e-mail.
>
>     What do you mean by finite T effect in MD? Kinetics?
>
>
>
> I mean thermal motion. You have an optimal structure/energy at 0K in 
> QM. In MD you want to simulate at higher T, I guess. The optimal 
> structures in both cases may be very similar, but may be not so 
> similar. I am just saying that you should not expect ideal coincidence 
> of energy vs. distance curves.
>
>     For the reproduction of binding energy, I guess I know how to do
>     it using QM method. Simply, I just need to do three single point
>     calculations for complex,
>     ligands and ion, respectively.
>
>
>
> And correct for BSSE.
>
>     For MM method, it is similar, however, I am not sure I get get the
>     MM energy for just one ion.
>
>
>
> This energy is zero within classical MD, since you do not consider 
> electrons and nucleus, as you do in QM.
>
> Only one calculation is needed for MM. You define the charge groups, 
> such as "ion" and "ligand" and look at the interaction between them 
> (g_energy).
>
>
>
>
>
>     Is my understanding right?
>
>     Thanks for all your explanations and suggestions on this problems!
>
>     All the best,
>     Qinghua Liao
>
>
>     On 04/09/2013 10:03 AM, Dr. Vitaly Chaban wrote:
>>
>>
>>
>>     On Tue, Apr 9, 2013 at 9:39 AM, fantasticqhl
>>     <fantasticqhl at gmail.com <mailto: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 <mailto: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
>>>
>>>
>>>
>>>
>>
>>
>
>