[gmx-users] minimization problem
Mark.Abraham at anu.edu.au
Mon Oct 26 01:08:51 CET 2009
Paymon Pirzadeh wrote:
> I merged two simulation boxes,
Are you sure your error is not here? Inspect your result visually! :-)
All the atoms need to be inside the box and non-overlapping.
> and now I want to perform a minimization
> to remove the problems at their boundary! I have reduced the dt to
> 0.000000001 and emstep to 0.000000001 as well. But still I get the
> Reading file Ih0001_81_93_204_min.tpr, VERSION 4.0.5 (double precision)
> Making 1D domain decomposition 8 x 1 x 1
> Steepest Descents:
> Tolerance (Fmax) = 1.00000e-05
> Number of steps = 705032704
> t = 0.000 ps: Water molecule starting at atom 190501 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Wrote pdb files with previous and current coordinates
> Program mdrun_d_mpi, VERSION 4.0.5
> Source code file: pme.c, line: 518
> Fatal error:
> 3 particles communicated to PME node 7 are more than a cell length out
> of the domain decomposition cell of their charge group
> as part of my error message. Should I still reduce the mentioned
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