[gmx-users] question about torsional potential fitting

André Farias de Moura moura at ufscar.br
Wed Oct 8 21:41:29 CEST 2014

There is no such thing as absolute energies and you may safely set the
minimum energy in your profile to zero.
(parallel profiles are the same profile when it comes to compute forces,
for instance, since the constant term yields a null derivative)



On Wed, Oct 8, 2014 at 3:50 PM, Victor Rosas Garcia <rosas.victor at gmail.com>

> Hello everybody,
> I have calculated ab initio energies for a torsional potential that I
> want to fit to a Fourier series. I have calculated the difference
> between the ab initio energies and the forcefield with the torsion
> potential set to zero (lets call that "diff curve").  This gives me a
> somewhat jagged periodic function. I can then get a cosine series that
> parallels the shape of the diff curve, but it is displaced along the
> energy axis.
> see this plot
> https://drive.google.com/file/d/0B2K7fedV_ZFzM3hXZVhyS2VvYnM/view?usp=sharing
> If I shift the plot of the series, by adding a constant term, the fit
> doesn't look so bad, to me at least, as in the following plot
> https://drive.google.com/file/d/0B2K7fedV_ZFzRmlpcnZhckEtdUE/view?usp=sharing
> However, I cannot add that constant term in the itp file for my
> molecule. Is it enough if the energies calculated by the Fourier
> series are parallel to the diff curve?
> Best regards
> Victor
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.


Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090

More information about the gromacs.org_gmx-users mailing list