Broken pyGromosTools examples

[JoStoe]

Dear All, I tried to run the examples of the pyGromosTools, but they mostly did not manage to finish. Especially parts where the md++ engine is used, seem to fail.

A common error message is: ChildProcessError: SubProcess Failed due to returncode: 1

According to the omd files, the md++ engine finishes successfully, but the output name of the omd is weird: examples/example_files/Hvap_files/hvap/test_gas/1_emin/analysis/data/1_emin1_emin_1.omd

My setup: -Ubuntu 22.04 -Fresh environment installed with mamba according to the info on this github repository.

• Gromos md++ Version 2023-09-09
• Gromos++ Version 2023-09-09

I attach one of my failing jupyter notebooks.

The following example files are failing:

• examples/developer_examples/dev_example_gromos_simulation.ipynb (failed)
• examples/Simple_examples/pyGromosToolsDay.ipynb (failed)
• examples/example_gromos_qmmm.ipynb (failed)
• examples/example_hvap.ipynb (failed)
• examples/example_solvation_free_energy.ipynb (failed)
• examples/example_TI_gromos_simulation.ipynb (failed)
• examples/tutorial_gromos_pipeline.ipynb (failed)

I hope to be able to use pyGromosTools soon. Best, Johannes tutorial_gromos_pipeline.zip