[gmx-users] error about x of the xxx bonded interactions could not be calculated ....

[Chang Woon Jang]

Dear Mark Abraham,

   Thank you for your advice.

When I did "mdrun -s topol.tpr -rerun conf.gro", the following warnings are
present.


Do you think that this is the problem? I have two tabulated bond potentials
(A-B, C-D) and two tabulated angle potentials (A-B-A, C-D-C). As you can
see, the only table_b1.xvg produced the warnings.

Does this mean that table_b1.xvg (A-B bonded potential) led the simulation
failure somehow?

Thank you.

Best regards,
Changwoon Jang

=====================================================

WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


WARNING: For the 1399 non-zero entries for table 0 in table_b1.xvg the
forces deviate on average 179% from minus the numerical derivative of the
potential


Back Off! I just backed up ener.edr to ./#ener.edr.2#
starting md rerun 'Built with Packmol', reading coordinates from input
trajectory 'confout.gro'

Reading frames from gro file 'Built with Packmol', 900 atoms.
Last frame          0 time    0.000

NOTE: 10 % of the run time was spent communicating energies,
      you might want to use the -gcom option of mdrun


               Core t (s)   Wall t (s)        (%)
       Time:        0.048        0.020      239.1
                 (ns/day)    (hour/ns)
Performance:        3.433        6.991

gcq#10: "Bum Stikkie Di Bum Stikkie Di Bum Stikkie Di Bum" (R. Slijngaard)



On Fri, Jan 29, 2016 at 11:27 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> You should verify that your tables implement the model you think they do.
> Use http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
> calculations on two-particle systems to verify you can reproduce trivial
> energies and forces.
>
> Mark
>
> On Fri, 29 Jan 2016 17:17 Chang Woon Jang <changwoonjang at gmail.com> wrote:
>
> > Dear Gromacs Users,
> >
> >    I am simulating coarse grained polymer systems with tabulated
> potential
> > (A B C D types).
> >
> > To obtain pair potentials, Iterative Boltzmann Inversion is used with
> > Gromacs.
> >
> > After 14 step (each step runs 1 ns (1000000) with time step 1 fs -
> 0.001),
> > the simulation had failed with the following error.
> >
> > x of xxx bonded interactions could not be calculated ....
> >
> > It sounds like Blowing Up problem. Therefore, I reduced the time step to
> > 0.0008 (0.8 fs), then the simulation failed at 164 step.
> >
> > I do not think that I started 1) a bad structure due to I equilibrated
> for
> > 120 ns at atomistic level, 2) inappropriate pressure coupling because I
> use
> > NVT ensemble.
> >
> > I am not sure what the following tip is in the gromacs website.
> >
> > "*your position restraints are to coordinates too different from those
> > present in the system,*"
> >
> >
> > I am using gromacs 5.0.8-dev-20151014-1f04b58
> >
> > Do you have any advice for solving this problem?
> >
> > I still keep decreasing the time step now at 0.0006.
> >
> > Thank you.
> >
> >
> > Best regards,
> > Changwoon Jang,
> > --
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-- 
Best regards,
Changwoon Jang,

Postdoctoral Research Fellow
Department of Chemical & Biological Engineering, Drexel University
3141 Chestnut Street, Philadelphia, PA 19104

Voice: (662) 617-2267
E-mail: cj395 at drexel.edu