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 <[email protected]
<mailto:[email protected]>> 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
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