[gmx-users] minimization problem

Paymon Pirzadeh ppirzade at ucalgary.ca
Mon Oct 26 00:31:24 CET 2009

I merged two simulation boxes, 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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