[gmx-users] default -rdd with distance restraints seems too large

Christopher Neale chris.neale at mail.utoronto.ca
Thu Oct 17 05:16:11 CEST 2013

I have a system that also uses a set of distance restraints

The box size is:
   7.12792   7.12792  10.25212

When running mdrun -nt 8, I get:

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 3.62419 nm

However, the largest restrained distance is 2.0 nm and the largest displacement between restrained atoms is 2.63577 nm

So why does mdrun set -rdd to 3.62419 nm ?

If I run mdrun -rdd 2.8 everything works fine.

Thank you,

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