[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 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. 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.

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
>
>
>
>