yank

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http://getyank.org/latest/yamlpages/options.html#yaml-options-number-of-equilibration-iterations 

jchodera

Now that [`mpiplus`](https://github.com/choderalab/mpiplus) is its own package, we should deprecate it here and start importing it from `mpiplus` so that our bugfixes can go there.

jchodera

Once the RMSD is released with the next version, we should reactivate that figure in the notebook.

andrrizzi

Free energy traces in notebook are wrong

1

The traces have made no sense/are not computed correctly since the SAMS refactor went in, this should be fixed

Lnaden

We should refactor YANK to not need OpenMolTools which is lagging behind the dev cycle. Might be a bit tricky since OpenMolTools provides the hook into Amber, Schrodinger, and OpenEye....

Lnaden

Now that conda-forge has done this, we should update the travis tests to Python 3.6 and 3.7, and deprecate 3.5.

jchodera

There are a couple of further optimizations that can be done here. 1. The temperature of the state is saved separately from the system in the dictionary `{system, temperature, pressure}`...

andrrizzi

We should add an option (`False` by default) to continue runs/setups that raised an exception.

andrrizzi

In follow up to #823, we want to make a YAML(s) which have the human-readable Cerberus schema's for the validators. There are a few steps to making this happen: 1....

Lnaden

Prevent users to specify a switch_experiment/phase_interval smaller than checkpoint_interval

1

When this happens the simulation never make progress because on the next cycle, it will resume from iteration 0 since no checkpoint was written before.

andrrizzi