[gmx-developers] Missing things in copy_QMrec?

[Ake Sandgren]

On Fri, 2009-12-11 at 10:56 +0100, Gerrit Groenhof wrote:
> > 
> > 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).

Ok, thanks for explaining things.
I'll take a look at all this to see if i can figure out if something can
be improved in the qm_gamess writing of input data.

-- 
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