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,
pb.
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
http://comppsi.csuohio.edu/groups/people/biswas.html
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