Irfan Alibay

[enchancement] always write out a PDB of the system that has all atoms present

1

There are quite a few occasions where having a copy of the system with all the atoms can be helpful (debugging, etc..). Since it's a single file we should try...

Follow-up from https://github.com/OpenFreeEnergy/openfe/pull/783

Example: https://docs.openfree.energy/en/latest/tutorials/index.html In the tutorial page we use different heading levels to put the tutorials into categories. Unfortunately it's very hard to see the difference between a top level heading...

_cc @hannahbaumann_ The userguide introduction is very specific to the idea of running a "workflow", and doesn't necessarily provide a lot of information about what else is in the userguide....

Add pymbar citations to duecredit

2

We should add those when we call `multistate_analysis` or just load up from results.

Barostat frequency should be optional

4

Given that gas phase calculations don't use barostats, then it might make sense to make the barostat frequency optional?

IntegratorSettings don't all apply to the MD Protocol

3

Looking at the IntegratorSettings, `reassign_velocities`, `n_restart_attempts`, and `constraint_tolerance`, don't get used in the PlainMDProtocol. This is because the PlainMDProtocol uses a LangevinMiddleIntegrator, whilst the RFE and AFE Protocols use LangevinDynamicsMove....