[gmx-developers] Missing things in copy_QMrec?

Gerrit Groenhof ggroenh at gwdg.de
Fri Dec 11 10:24:12 CET 2009

So, the idea was  to use the geometry optimization routines of the QM program. To model the environment explicity in these optimization, I included the MM atoms that have carge and/or LJ interactions. The coordinates, LJ parameters and charges are passed on the gaussian. Gaussian then performes the optimization. For simple systems this seems to work, although, as expected I get a different structure if I take a different snapshot from the MD. My naive idea was that I could do an MM simulation, takes snapshots and perform a transition state optimization. By averaging the height of the barrier over all MM snapshots, I though I could learn somethign about the effect of the environment.

However, in more complex systems, such as an enzyme, the optimization almost never converged, which I think is due to the too-strong LJ repulsion near the QM/MM interface.

Does this answer the question?


On 11 Dec 2009, at 10:05, Ake Sandgren wrote:

> On Fri, 2009-12-11 at 09:39 +0100, Gerrit Groenhof wrote:
>> I have not seen this interface. The way I set it up for gaussian (but it might be broken), was that gromacs passes coordinates charges and LJ parameters to gaussian. The MM atoms are then kept at ther positions, while the QM atoms optimize. The QM/MM interaction was thus done in gaussian. I don't know about the latest gamess version, but for a simulatanous MM optimization, the complete MM machinery needs to be implemented in the qm program, which I was too much work at the time.
>> Also, more philosophically maybe, one (or at least I) can argue how useful mimizations are for protein systems.
> Since my understanding of this is fairly limited still I will pester you
> with more questions.
> What exactly do you mean with "while the QM atoms optimize"? Geometry
> wise or what?
> And what are the LJ parameters (the c6/c12 values?) and what are they
> used for (in gaussian)?
> -- 
> Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> Internet: ake at hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90 7866126
> Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
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Gerrit Groenhof
MPI biophysical chemistry

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