Equilibration protocols

[jmichel80]

Currently the equilibration protocol in BSIigprep.py used by the RBFE pipeline does not wrap coordinates. This makes it difficult to visually inspect equilibrates boxes to check for issues with ligand binding modes before running FEP calculations.

Ideally the pipeline would include a step to wrap coordinates such that binding sites can be more easily visualised.

[annamherz]

Hello! In the newer branches of BSS (feature-amber-fep, benchmark-2022), coordinates are automatically wrapped in Amber using iwrap=1 in the config file for any equilibration runs (as long as they are not also Free Energy runs). Should there be an additional function in BSS for wrapping coordinates as well? As far as I am aware I don't think there is currently a specific function for it