[GaMD-discuss] implementation of unit cell fix for orthorhombic PBCs in openMM GaMD

[Blake M. <me...@al...>]

Hello,

I generated a rhombic dodecahedron cell in openmm-setup. When I went to run
openMM-GaMD, I got the following error:

gamdRunner -d 2 xml lower-dual1.xml
Traceback (most recent call last):
  File "/usr/local/bin/gamdRunner", line 83, in <module>
    main()
  File "/usr/local/bin/gamdRunner", line 74, in main
    gamdSim = gamdSimulationFactory.createGamdSimulation(
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/media/bak11/binaries/git/gamd-openmm/gamd/gamdSimulation.py", line
255, in createGamdSimulation
    gamdSimulation.simulation.context.setPeriodicBoxVectors(
  File
"/media/bak11/binaries/miniconda3/envs/openmm/lib/python3.12/site-packages/openmm/openmm.py",
line 11994, in setPeriodicBoxVectors
    return _openmm.Context_setPeriodicBoxVectors(self, a, b, c)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Periodic box vectors must be in reduced form.

The fix to this error in openMM8 was documented in the following issue on
their git page: https://github.com/openmm/openmm/issues/4515

where they have added a definition to unitcell.py to fix the issue:
https://github.com/openmm/openmm/blob/2d4372d7ba8de7e02b4af9cb57f4ef29cd146f34/wrappers/python/openmm/app/internal/unitcell.py#L83-L97

Is there a similar call in the codebase for gamdRunner that could be
modified to handle non-cubic PBCs out of the box?

Blake
-- 

Principal Scientist

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Adjunct Professor

C. Eugene Bennett Department of Chemistry

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