[gmx-developers] Missing things in copy_QMrec?

[Gerrit Groenhof]

I think it is important to understand if gamess performes such an optimization or not.

In addition, we need to know how bonded interactions are handled by gamess.

Maybe Huub can comment?

Gerrit


On 11 Dec 2009, at 11:02, Ake Sandgren wrote:

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