[gmx-developers] Missing things in copy_QMrec?

[Gerrit Groenhof]

> 
> Well at least most of them, although it creates more questions due to my
> lack of understanding :-)
> 
> 1 - what are the LJ parameters?

Parameters for the Lennard-Jones potential, i.e. C6 and C12. This potential describes the dispersion and repulsion between atoms, the so-called Van der Waals interactions

> 2 - "perform a transition state optimization" that would be the bTS
> flag?

Yes.


> 3 - "height of the barrier" is that a cut-of where they should be
> ignored or something?

No, the height of the barrier between the reactants and products on the potential energy surface.
The rate of a reaction is determined by the barrier, which in turn can be influences by the environment (the protein).

Gerrit




> 
> 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
> 
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--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/