[gmx-users] Volume Contraction Issue
2018-12-07 21:08:26 UTC
I'm currently trying to run a semi-isotropic NPT simulation where one
dimension of the box changes in size over a fairly wide range
throughout the course of the multiple successive trajectories run on a
given node. One issue I keep running into is that after a certain
point, the box has changed dimensions enough that the initial
processor decomposition used in the first trajectory no longer works
for the reduced box size, and GROMACS terminates with an error about
not being able to use the assigned processors to construct a domain
decomposition when it tries to create the tpr file for the next phase
of the simulation.

This is a frustrating error to deal with manually, and it would make
sense to have the system adapt to its changing size by changing the
number of processors used. Is there a way to tell GROMACS to handle
extra processors more gracefully - for example by ignoring some
available cores in order to obtain a correct decomposition? The error
messages only suggest ways to change the desired domain size for the
simulation and it's not clear to me a priori what size would work
throughout an entire simulation, or if such a decomposition exists
without changing the number of processors available.

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