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

[Mark Abraham]

Hi,

That seems extremely likely. Prove your tables work on something trivially
simple.

Mark

On Fri, 29 Jan 2016 17:51 Chang Woon Jang <changwoonjang at gmail.com> wrote:

> 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
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