VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Wed Nov 18 2015 - 14:31:22 CST

Hi Christopher,

Thanks for the explanation. Actually, the roughness is more a result of me
fiddling around with the dihedral parameters (the "r02" in the plot legend
is misleading, I have done it multiple times, including writing to a
temporary par file and starting over from those parameters). The first few
refittings did not generate such a rough plot.

I am still having a hard time getting the plots to match exactly. Just to
clarify, it is the positions of the maxima/minima that matter the most,
right? Not the actual value of the energy at each point (i.e. exact
overlap)?

Also, what does the "RMSE" in the fitting window indicate? Is it something
like the mean-squared deviation, in that I should try to achieve as low a
value as possible? Is there an approximate cutoff (something like, my RMSE
must be below a certain number to be reliable)?

Regards,
Chitrak.

On Wed, Nov 18, 2015 at 3:08 PM, Mayne, Christopher G <cmayne2_at_illinois.edu>
wrote:

> Chitrak,
>
> Those types of discontinuities are not uncommon. They are indicative of
> major structural changes as the result of crossing some energy barrier
> during the scan. The roughness of the MM PES, however, is a little odd. I
> would recheck bonds and angles, if you parameterized any, as the dihedral
> PES is often where trouble with earlier parameters will often show up.
>
> Regards,
> Christopher Mayne
>
> > On Nov 18, 2015, at 8:07 AM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:
> >
> > Hi VMD users,
> >
> > I am trying to parameterize a unnatural amino acid using FFTK. I am at
> the dihedral fitting stage. I only have one new dihedral to fit.
> >
> > What I find strange is that the QME plot has discontinuities. I ran the
> Gaussian jobs with 5 degree step and 2 degree step, but both the times the
> discontinuities persisted. Is this normal, or has someone else had this
> issue as well?
> >
> > I have attached the QME plot here.
> >
> >
> >
> > Best regards,
> > Chitrak.
> > <Fitting.pdf>
>
>