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

[fantasticqhl]

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?

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. For MM method, it is similar, however, I 
am not sure I get get the MM energy for just one ion. 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
>>
>>
>>
>>
>
>