[gmx-developers] Missing things in copy_QMrec?

[Ake Sandgren]

On Fri, 2009-12-11 at 10:24 +0100, Gerrit Groenhof wrote:
> 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?

Well at least most of them, although it creates more questions due to my
lack of understanding :-)

1 - what are the LJ parameters?
2 - "perform a transition state optimization" that would be the bTS
flag?
3 - "height of the barrier" is that a cut-of where they should be
ignored or something?

I'll try to find a local QM person if possible so explain things in more
detail.

-- 
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