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

Mark Abraham mark.j.abraham at gmail.com
Tue Feb 20 11:20:23 CET 2018


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, 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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