[gmx-users] For non-zero entries for table x, the forces deviate from minus the numerical derivative of the potential
douwepollmann at gmail.com
Tue Feb 20 15:49:16 CET 2018
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?
2018-02-20 11:20 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
> 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.
> On Tue, Feb 20, 2018 at 10:37 AM Douwe Pollmann <douwepollmann at gmail.com>
> > 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,
> > 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
> > non-bonded potentials, while this dihedral is of course a bonded
> > 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
> > 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
> > too much..
> > Thank you very much in advance!
> > Kind regards,
> > Douwe Pollmann
> > --
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