[gmx-users] force constants

[Lars Schaefer]

Arturas wrote:

> Hi,
> 
> I am wondering how force constants are derived for various FF in
> GROMACS. I want to get the force constant for Fe=O bond. I tested C=O
> force constant for Fe=O in my model and it worked well. Now I want to
> supply Fe=O bond parameters for FF, which are right for that model.
> 
> Are they just calculated from Hook law knowing the experimental
> vibration frequency (cm-1) ? If YES, Are they modified to achieve
> good MD results ?

Hm, I'm not completely sure about that. But especially in asymmetric 
molecules, the normal modes are often pretty delocalized over larger 
parts of the molecule, so an experimental frequency might not be 
uniquely assigned to be "only" the Fe=O bond strech mode you want.
I think, e.g. in the case of a diatomic (i.e. assuming a localized 
bond-stretch-mode), the force constant can be derived via omega = 
sqrt(k/m) with m being the reduced mass.

> 
> Are they calculated from QM/ab intio methods ? If YES, what are
> advises ?

You could either gain the FF from the Hessian (either before or after 
diagonalization, and either from the "normal" or the inverted one, think 
there are some discussions around about that issue, see e.g. Grunenberg 
et al), or / and you could perform a (relaxed) PES scan along the bond 
you are interested in and afterwards fit a harmonic to that energy.

Cheers, Lars

> 
> 
> With best
> Arturas
> 
> 
> 
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.

-- 
*******************************************************
Lars Schaefer, PhD student                            *
MPI for biophysical Chemistry                         *
Theoretical and computational Biophysics group        *
Department 070                                        *
Am Fassberg 11, D-37077 Goettingen                    *
Tel: 0049 551 201-2305, Fax: 0049 551 201-2302        *
E-Mail: Lars.Schaefer at mpi-bpc.mpg.de                  *
Home: http://wwwuser.gwdg.de/~lschaef2/homepage.html  *
*******************************************************