[gmx-users] mdrun error

[Mark Abraham]

Hi,

Is your box changing shape? You've switched from isotropic to anisotropic,
and to a thermostat that is not tolerant of changes to the size/shape of
the box. Change one thing at a time.

Mark

On Sun, Jun 12, 2016 at 8:09 PM mahdiyeh poorsargol <
poorsargol.m64 at gmail.com> wrote:

> Dear gmx users,
> I am using gromacs 4.6.5 to simulate a system including: graphene + water +
> surfactant. I used the box with size 7.4,7.4,9.4 (nm3) and a cutoff
> distance of 1.2 nm. I have done nvt with Berendsen thermostat for 1 ns ,
> npt with Berendsen thermostat and Berendsen barostat for 2 ns (pcoupltype=
> isotropic). when I mdrun with Nose-hoover thermostat and Parrinello-Rahman
> barostat for 40 ns (pcoupltype= anisotropic), it gave me the following
> error:
>
>
> Fatal error:
> Step 109048: The X-size (0.679861) times the triclinic skew factor
> (1.000000) is smaller than the smallest allowed cell size (0.679862) for
> domain decomposition grid cell 4 0 1
>
> I would be pleased if anyone could help me how to fix this.
> mahdiyeh
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