[gmx-users] Error in NVT equilibration

[Dallas Warren]

As the warning indicates, due to the bond force constant and atom masses,
it will oscillate too fast for the time step. And as you found out, exactly
that happened and the system exploded. There are two ways that you can
"fix" that (reduce time step or bond force constant), but wouldn't
recommend either at this point. You need to look into the source of the
topology, how it was generated, why that force constant is applied to that
bond etc.

On Fri, 14 Sep. 2018, 11:06 pm Gonzalez Fernandez, Cristina, <
cristina.gonzalezfdez at unican.es> wrote:

> Dear Gromacs users,
>
>
> I am trying to perform a nvt equilibration, but when I generate the .tpr
> file I get a warning indicating that a bond is oscillating too fast:
>
>
> The bond in molecule-type MOL_1 between atoms 38 C21 and 39 O22 has an
> estimated oscillational period of 2.4e-02 ps, which is less than 5 times
> the time step of 1.5e-02. Maybe you forgot to change the constraints mdp
> option.
>
>
>
> I have ignored it with the -maxwarn option and I obtain the .tpr file.
> However, when I run the simulation I obtain this error?
>
>
> Too many LINCS warnings (1630)
>
>
>
> Are the error and the warning related? How could I solve the Lincs error
> and the warning?
>
>
> I attach the .mdp file.
>
>
>
>
> Thank you in advance,
>
>
> C.
>
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