[gmx-users] QM/MM features

Pradip Kumar Biswas p.biswas at csuohio.edu
Tue Feb 21 22:36:01 CET 2006

Hi Yolanda,

Sometimes back I discussed the issue of transition states with Gerrit 
understood that it is not yet implemented in any of his interfaces 
though he
is interested to. And this is true for Gromacs-CPMD qmmm as well. They 
offer mdrun energy minimization and simulation for the whole system 

Ps. As far as Gromacs-CPMD qm/mm is concern I can see one possibility 
That is using CPMD metadynamics to find the transition state for the QM 
while the MM environment is added as an external field to the QM. Now 
can adopt  a perturbative approach by coming back to Gromacs, making 
the move
of the atoms (QM+MM) and then again go to CPMD metadynamics; and repeat
till the energy of the transition state converges. I can not say how 
far it makes sense
as I have not done any calculation but I see it is a possibility 
without seeking a lot
of changes in the codes.


On Feb 21, 2006, at 2:33 PM, YOLANDA SMALL wrote:

> Hello users,
> I believe that Gerrit is out of town at the moment so if anyone else 
> knows the
> answer, I would appreciate your feedback.
> I would just like to clarify a detail about the QM/MM features:
> At the moment, is the code only capable of doing QM/MM MD with surface 
> hopping
> but not with QM transition state seaches or optimizations?
> If so then is the code only capable of doing QM/MM transition state 
> seaches and
> optimizations with energy minimization of the MM region and not MD on 
> the MM
> region?
> Thanks,
> Yolanda
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