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 <fantastic...@gmail.com
<mailto:fantastic...@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
<fantastic...@gmail.com <mailto:fantastic...@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
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