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