[gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L
fantasticqhl
fantasticqhl at gmail.com
Tue Apr 9 11:03:55 CEST 2013
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
>>
>>
>>
>>
>
>
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