AMBER Archive (2008)

Subject: Re: AMBER: Azobenzene: dihedral angle CCNN force field parameter

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Sat Apr 26 2008 - 16:10:25 CDT

Let's make sure we all understand what these torsional potentials mean.

They are NOT the true torsional potential that the system feels if
computed under the 'perfect force field' or a great QM hamiltonian.

They are in fact, a fudge factor introduced to correct for imperfections
in the force field.

So, there WILL be a barrier even if the torsional potential has a zero
force constant.

Now, is this barrier good enough, and are the minima in the correct
place? To answer that you must do a torsional potential scan with a good
QM method, and compare that energy profile with what the force gives you
with a 'zero' torsional potential.
The difference between those two calculations in then fit with a fourier
series. Voila, you got your tosional potential then.

a.

Chih-Ying Lin wrote:
>
> Hi
> I found that the dihedral CCNN force field for the azobenzene are not quite right.
> 0 3.14 3.0 :1_at_CAH :1_at_CAM :1_at_NAK :1_at_NAL (9,11,12,13)
>
> With this set of parameters, the two phenl rings can rotate freely.
> Any one have idea for this?
>
> Thanks
> Lin
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
============================================================================

To announce that there must be no criticism of the president,
or that we are to stand by the president right or wrong,
is not only unpatriotic and servile, but is morally treasonable
to the American public."
   --  Theodore Roosevelt
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu