[gmx-users] Fwd: QMMM calculation

[Pradip Kumar Biswas]

Hi Christian,

Thanks for clarifying the point. You are right. The interface does not 
put back the removed non-polar hydrogens. It is designed for all atom 
FF.

Now, even if I find a way to add the removed non-polar atoms  in the 
interface, there needs to have a careful consideration of the forces on 
the polar atoms when you transfer the forces to Gromacs from QM. 
Supposing that while coming back to MM from QM you care only for the 
forces on the polar atoms as the MM part is satisfied only with them, 
it is perhaps easily doable. I need to think about the energy 
conservation issue, though.

Alternately, you need to have an admixture as you have said: all-atom 
QM part with united-atom MM part. How difficult it will be to generate 
topology and coordinates for such a case? What other problem(s) you 
foresee?

thanks,
pb.

On Jun 17, 2006, at 1:47 PM, Christian Burisch wrote:

> Pradip Kumar Biswas wrote:
>
> Hi,
>
>>> calculation. I have seen you using OPLS for your calculation. Is it
>>> possible to use Gromos force field, where polar hydrogen is used.
>
>> You should be able to use any force field implemented or supported by 
>> Gromacs. QM/MM does not depend upon the force field.
>
>> I could not really get what you mean.
>
> since I am interested in this topic, too, but without having used your 
> interface yet: I guess the question is where do the nonpolar hydrogens 
> (which usually are missing in GROMOS united atoms ff, so you cannot 
> put them in the [QM] index group) come from when switching from MM to 
> QM? Are they added e.g. from geometric criteria by your interface or 
> CPMD (I guess not), are they just ignored (definitely not) or do one 
> has to generate an all-atom QM part of the system in the first place 
> (i.e. coordinates and topology; I guess this is the case)? That would 
> mean a mixture of united- and all-atom ff.
>
> Regards
>
> Christian
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--
Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
Phone: 1-216-875-9723
http://comppsi.csuohio.edu/groups/people/biswas.html
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