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

[Mark Abraham]

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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