[gmx-users] Replica Exchange Error

[Joe Joe]

Hi All,
I get the following error when running replica exchange. I have 32 replica's
with each replica running on 4 processors (128 total). How do I decrease the
domain decomposition cell size, -dss? What should I set it to?

Thanks,

Ilya

DD cell 2 0 0: Neighboring cells do not have atoms: 22217 20764 20762 21782
21780 22244 22249 21863 21734 21739 22223 22240

DD cell 3 0 0: Neighboring cells do not have atoms: 21856 21868

DD cell 4 0 0: Neighboring cells do not have atoms: 21807 21809

DD cell 5 0 0: Neighboring cells do not have atoms: 22240 21765 20764 20762
21253 21250 21863 21860 22246 22251 21771 21789
DD cell 7 0 0: Neighboring cells do not have atoms: 21858 22221 21736

DD cell 0 0 0: Neighboring cells do not have atoms: 21789 21811 21253 21769
21742 21724

DD cell 7 0 0: Neighboring cells do not have atoms: 22221 21742
DD cell 1 0 0: Neighboring cells do not have atoms: 22223 22240
DD cell 2 0 0: Neighboring cells do not have atoms:
DD cell 4 0 0: Neighboring cells do not have atoms: 21807 21809 20764 20762
21782 21780 21739 21745 21722 21727

DD cell 5 0 0: Neighboring cells do not have atoms: 21765 20764 20762 21253
21250 21863 21860 21771 21789

-------------------------------------------------------
Program mdrun_mpi, VERSION 4.0.4
Source code file: domdec_con.c, line: 679

Fatal error:
DD cell 5 0 0 could only obtain 96 of the 108 atoms that are connected via
vsites from the neighboring cells. This probably means your vsite lengths
are too long compared to the domain decomposition cell size. Decrease the
number of domain decomposition grid cells or use the -rcon option of mdrun.
-------------------------------------------------------

"Live for Liposuction" (Robbie Williams)

Error on node 45, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 45 out of 128

-------------------------------------------------------
Program mdrun_mpi, VERSION 4.0.4
Source code file: domdec_con.c, line: 679

Fatal error:
DD cell 0 0 0 could only obtain 40 of the 45 atoms that are connected via
vsites from the neighboring cells. This probably means your vsite lengths
are too long compared to the domain decomposition cell size. Decrease the
number of domain decomposition grid cells or use the -rcon option of mdrun.
-------------------------------------------------------

"Live for Liposuction" (Robbie Williams)

Error on node 40, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 40 out of 128
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