Mark J. Williamson

Hi John, I could probably help with the JUnit 5 bit; I've done a few JUnit 4 to 5 migrations recently.

Dear Marcus, Apologies for the delay in replying. Thank you for the explanation and I will follow your advice re switching to JSON dumps. Thanks, Mark

Many thanks for the explanation and debugging tip.

With --stacktrace and Ubuntu 20.04.3 and openjdk-17, I see: ``` ... Caused by: java.lang.IllegalAccessException: module java.base does not open java.lang to unnamed module @4d154ccd at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at...

This might be related to the recent [top level Python package rename in OpenMM 7.6](https://github.com/openmm/openmm/releases/tag/7.6.0). Try installing an earlier version of OpenMM to your conda environment, e.g.: ``` conda install...

[edit]I think this may be resolved with the OpenMMTools 0.21.0 [release](https://github.com/choderalab/openmmtools/releases/tag/0.21.0)?

Ah apologies; I've jumped the gun a bit; thank you for the link.

See also https://github.com/conda-forge/yank-feedstock/issues/1

> There's a fast and simple script that doesn't use openmmtools at http://openmm.org/tutorials/alchemical-free-energy/ - how about changing your script to use the same system and annihilate a single particle? One...

Are you both still seeing this with OpenMM 7.7.0 and OpenMMtools 0.21.0? I am seeing something similar with an internal test system and want to debug this more. Just so...