[gmx-users] Fwd: QMMM calculation

Pradip Kumar Biswas p.biswas at csuohio.edu
Sun Jun 18 21:48:21 CEST 2006

Hi Christian,

Thanks for your comments. I am writing to Axel (he is now in upenn, US) 
as he might be having the first hand experience of how CPMD-Gromos 
interface manages the issue.

best regards,

On Jun 17, 2006, at 5:45 PM, Christian Burisch wrote:

> Pradip Kumar Biswas wrote:
> Hi Pradip,
>> 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.
> sounds good! You would need some kind of special hydrogen database for 
> applying the protons. Perhaps one could use a modified ffgmx2.hdb for 
> that.
>> 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?
> Coordinates should be no problem, if one edits GROMACS' hydrogen 
> database or adds the protons by an external editor like PyMol.
> Concerning the topology one would have to generate some "new" all-atom 
> amino acids (if these are included in the QM box) and ligands. One 
> could perhaps use the "bare carbon" atom types C and CB for that, but 
> I don't know if there is a proper hydrogen type.
> Another disadvantage would be that you cannot use the great PRODRG 
> service for automatized topology generation, since this tool "only" 
> generates united-atom parameters for the GROMOS96 43A1 ff (of course).
> But IIRC some half years ago there was an announcement/rumour of 
> PRODRG being capable of generating OPLS-AA topologies in the near 
> future. In this case one could switch to this ff completely without 
> having to generate ligand topologies from scratch.
>> What other problem(s) you foresee?
> Mmmh, personally I would try to avoid a hybrid all-/united-atom ff (I 
> always try to stay as close as possible to the standard ff 
> parameters). But since people seem to use e.g. united-atom lipids and 
> all-atom proteins (OPLS-AA) together without problems this is perhaps 
> only a fad of mine.
> Perhaps Axel Kohlmeyer (who is on this list, too) could comment on the 
> topic? He's been in the department next door and AFAIK they use a 
> GROMOS96/CPMD interface over there. Of course I could walk over to the 
> next building and ask them personally... ;-)
> 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
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