[gmx-users] Reg:1 particles communicated to PME node 0 are more than 2/3 times the cut-off

[Mark Abraham]

On Fri, Feb 8, 2013 at 7:48 AM, Subramaniam Boopathi
<boopathiphd at gmail.com>wrote:

> dear sir,
>            how can i remove this following problem
>


>    Energies (kJ/mol)
>           Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     2.36059e+03    3.53976e+02    7.34586e+00    7.00084e+03    2.02621e+03
>         LJ (SR)   Coulomb (SR)   Coul. recip. Position Rest.      Potential
>     7.70414e+03   -5.91044e+04   -6.76092e+03    1.80260e+00   -4.64104e+04
>     Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
>     6.48550e+04    1.84446e+04    1.84446e+04    1.88479e+03    7.32453e+03
>    Constr. rmsd
>     4.81184e-01
>
>
> -------------------------------------------------------
> Program mdrun_d, VERSION 4.5.5
> Source code file: pme.c, line: 538
>
> Fatal error:
> 1 particles communicated to PME node 0 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension y.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>

Did you try following the link mdrun suggested? :-)

Mark