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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