[gmx-users] For non-zero entries for table x, the forces deviate from minus the numerical derivative of the potential

[Mark Abraham]

Hi,

The simplest explanation is that the check is missing that factor, but we
don't yet know that you have tested that the computed forces agree with
your intention in the construction of the table. The computed energies are
not an adequate test. To do that, you need to write the forces using an
.mdp file with nstfout set, and that is best done via mdrun -rerun as I
suggested.

Mark

On Tue, Feb 20, 2018 at 3:49 PM Douwe Pollmann <douwepollmann at gmail.com>
wrote:

> Dear Mark,
>
> Thanks for your reaction!
> I have put the dihedral in a test system, where I freeze the positions of
> the atoms and calculate the energy of the system with the Tab.-Dih. option
> in gmx energy.
> The only dihedral in the system is  the one from my own table, and the
> values are in pretty good agreement (deviations of a few percent) with the
> values I would expect.
> So it seems that the interpolation is done correctly, but the strange thing
> is that I still get the warning that the forces deviate on average 196%.
> On one side it is positive that the dihedral energies are correct, but I
> still don't know what the issue is concerning the warning..
> Do you (or someone else) have any other ideas about it?
>
> Best,
> Douwe
>
>
> 2018-02-20 11:20 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
>
> > Hi,
> >
> > It looks like somebody is missing a factor of 2; either you, or the check
> > in the table code, or maybe also in the evaluation kernel. I suggest you
> > set up a three-particle system, and make some coordinate files with those
> > particles at carefully chosen angles and see what energy and force is
> > returned by
> >
> > mdrun -s your.tpr -table yourtable.xvg -rerun your.gro
> >
> > Halve the values in the force column if you have to in order to get a
> force
> > output and understand what the issue really is.
> >
> > Mark
> >
> > On Tue, Feb 20, 2018 at 10:37 AM Douwe Pollmann <douwepollmann at gmail.com
> >
> > wrote:
> >
> > > Dear Gromacs users,
> > >
> > > I am currently trying to implement a user-defined dihedral into a
> coarse
> > > grained model (in version 5.1.4), but I get the following error:
> > >
> > > 'For the 35988 non-zero entries for table 0 in tables/table_d4.xvg the
> > > forces deviate on average 196% from minus the numerical derivative of
> the
> > > potential'.
> > >
> > > The three columns in table_d4 are the angle [-180, 180], the potential
> > > energy (in kJ/mol) and minus the derivative (first I had +derivative,
> > which
> > > resulted in an error or 204%). If I am correct, Gromacs interpolates
> its
> > > own function through the data points given in table_d4, but the result
> is
> > > far from correct in this case.
> > >
> > > I have tried to use -debug during mdrun to get the interpolated values
> of
> > > Gromacs, but I only get the values (ctab.xvg, dtab.xvg and rtab.xvg) of
> > the
> > > non-bonded potentials, while this dihedral is of course a bonded
> > potential.
> > >
> > > In section 6.10.1 of the manual (version 5.1.4) it is mentioned that
> > > 'Gromacs stores A0, A1, A2 and A3', the parameters of the interpolated
> > > cubic spline. My question is if any of you knows if it is possible to
> get
> > > these parameters, or if it is possible to get the functions
> interpolated
> > by
> > > Gromacs, to check where the mistakes are made.
> > > If this is not possible at all, do you have any ideas how I can
> decrease
> > > the deviation of the forces? 0% deviation is not needed, but 200% is a
> > bit
> > > too much..
> > >
> > > Thank you very much in advance!
> > >
> > > Kind regards,
> > > Douwe Pollmann
> > > --
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