[gmx-users] Error in minimisation

hasthi durgs7krish at gmail.com
Sat Feb 1 08:26:54 CET 2014

Dear GROMACS users,
                                  I am running membrane protein simulation.
I have shrunk the area with the help of inflate.pl script.When I run energy
minimisation I get this following error...

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Step=    0, Dmax= 1.0e-02 nm, Epot=         -nan Fmax= 9.20610e+05, atom=
Program mdrun, VERSION 4.6.1
Source code file: /home/guest/gromacs-4.6.1/src/mdlib/pme.c, line: 827

Fatal error:
2 particles communicated to PME node 6 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.

What might be the cause for this? I could not figure it out. Please help me


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