[gmx-users] domain decomposition failure

[Harry Mark Greenblatt]

BS”D


Dear All,

  I have now run into this issue with two very different systems (one with 762 protein and 60 DNA residues, the other with 90 protein residues).  If I try and carry over the velocities from the final equilibration step into a production run, and try to use more than one MPI rank, I get an error like

Not all bonded interactions have been properly assigned to the domain decomposition cells
A list of missing interactions:
                Bond of   7320 missing     41
               Angle of  25159 missing    193
         Proper Dih. of  39680 missing    450
       Improper Dih. of   2524 missing     15
               LJ-14 of  35682 missing    286

and the job hangs.

This occurs in Version 2019.4 and 2019.5, and both systems were solvated with water and ions, and neutralised wrt charge.

The only way to proceed is to either:

1.  Run one MPI rank (rather slow)

or

2.  Set
  continuation   = no
  gen_vel    = yes

I presume the desirable thing to do is to carry over the velocities, but that does not seem to work properly.  I can provide more details to the developers, if this appears to be abnormal behaviour.

Thanks


Harry



--------------------------------------------------------------------
Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology           harry.greenblatt at weizmann.ac.il<mailto:harry.greenblatt at weizmann.ac.il>
Weizmann Institute of Science        Phone:  972-8-934-6340
234 Herzl St.                        Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel