[gmx-users] Bond Decomposition Error

tca1 tca1 at rice.edu
Thu Nov 8 19:44:32 CET 2018

Hi everyone,

I've recently gotten a simulation of a 2D crystal surface set up in  
GROMACS using a combination of x2top and periodic-molecules. Things  
run okay for me when I do small-scale tests on a single core  
(minimization, NVT equilibration, etc), however when I try to scale  
this up and run it on multiple processors I get an error saying:

Not all bonded interactions have been properly assigned to the domain  
decomposition cells

This happens for any number of cores larger than 1, and it happens  
even during my minimization step. I don't believe this is the result  
of a poor equilibrium geometry, because when I run intermediate-sized  
tests on a single core, they finish correctly after only a handful of  
steps, even using fairly tight minimization settings. Additionally,  
the box itself is simple - just a cube with periodic boundary  
conditions applied - and I'm leaving out everything but the crystal  
surface in the simulation to reduce the complexity for debugging.

I suspect the error has something to do with the periodic-molecules  
option and an unidentified oversight in my job setup, but I have no  
idea where to look. Does anyone have any suggestions?

Tom Allen

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