Molecular Dynamics Simulation 6 Molecular dynamics 6 Free energy 4 Ligand migration 4 Ligands 4 MSMD 4 Proteins 4 Thermodynamics 4 computer simulation 4 hemoprotein 4 implicit ligand sampling 4 ligand 4 ligand migration 4 molecular dynamics 4 nitric oxide 4 nitrophorin 4 priority journal 4 protein function 4 thermodynamics 4 3 nitrotyrosine 2 AMBER 2 Binding Sites 2 CO 2 Carbon Monoxide 2 Catalytic Domain 2 Computer Simulation 2 Dissociation 2 Dynamics 2 Enzyme Activation 2 Enzyme inactivation 2