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create a new conda environment on any machines that will hold your local QCArchive server or run compute managers using the command:
conda env create openforcefield/openff-benchmark-optimization
activate the environment using
conda activate openff-benchmark-optimization
It is recommended to use this conda package as any Any update to the workflow will be distributed via an update to this environment.
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to start the server and the error cycling machinery which will periodically check all running tasks in the archive and restart them when an unexpected error is found using the following command.
Troubleshooting
Where is the local QCArchive database stored
you can find the database in a path like
.qca/qcfractal/on the machine where you activated the server.
Why do I see stereochemistry issues in the initial step in the workflow?
All file reading and writing is done via the Open Force Field Toolkit which is powered by RDKit. When we read in a molecule we check according to RDKits definitions if the molecule has any missing stereochemistry. We recommend using 3D SDF files where possible so that all stereochemistry is fully defined.
Missing molecules?
During the workflow, multiple things can go wrong manly involving undefined stereochemistry when this happens a warning is shown about the molecule is moved to an error directory to keep track of.
During the analysis, you may notice some molecules are missing or the number of conformers of the molecule is not as expected. During optimization, we sometimes see proton transfer and the resulting optimized geometry is actually a tautomer of the input, in this case, the optimization is excluded from the analysis. This should not affect the results.
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