[meta] Membrane support in OpenFE Protocols about openfe HOT 2 OPEN

Plus one for this @IAlibay

from openfe.

Just to add to the discussion in case it's interesting, I have done a dirty fix to run a membrane system in https://github.com/frannerin/openfe/tree/membrane (and it has worked for me).

Basically, as a .pdb for my protein component I include protein-membrane-waters pre-equilibrated, saving only waters up to ~5A away from protein or membrane, i.e. the fine-tuned solvation shell.

Then, I added to the OpenMMSolvationSettings in openfe/protocols/openmm_utils/omm_settings.py an option to pass a boxSize to fill the remaining volume with waters during the normal system setup. In openfe/protocols/openmm_utils/system_creation.py I added an "if" clause to pass that boxSize to the addSolvent method (boxSize is already an argument of it) if the system being setup is the complex one and boxSize has been passed; or use the padding argument otherwise (soluble protein or ligand system).

I also added an xtal_water_residues argument to SolvationSettings to be able to specify the residue names of my "xtal" waters so that they are correctly handled/kept around using addSolvent (my waters are named T3P).

In settings.forcefield_settings.forcefields I add amber/lipid17.xml and it recognizes POPC.

from openfe.