adapt some packages

[JohannesKarwou]

Some updates, so transformato and the CI workflow works again with the latest packages:

• update simulation.minimize to work with openmm=8.1 in the CI workflow
• use the new syntax of pymbar=4.0 (i.e. m.compute_free_energy_differences)
• remove the dependency in the CI github file

[codecov-commenter]

Codecov Report

Merging #117 (5182e93) into master (77d5f0f) will increase coverage by 0.04%. The diff coverage is 0.00%.

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Additional details and impacted files