Journal Article Proteins molecular dynamics BAR Bacteriochlorophylls Biopolymers GROMACS HPC Jarzynski Ligands Light-Harvesting Protein Complexes PDB manipulation PDB repair Photosynthetic Reaction Center Complex Proteins Quinones RRHO theory Research Support, Non-U.S. Gov't SAMPL challenges alchemical calculations docking drug design entropy gap handling missing residues non-equilibrium relative free-energy calculations scoring functions