Semi-grand canonical molecular dynamics simulation of bovine pancreatic trypsin inhibitor Original Research Article

In the quest to understand both the structural and thermodynamic facets of biomolecular–solvent systems semi-grand canonical ensemble molecular dynamics simulations of a protein in solution are performed. In these simulations only the water molecules in the system are allowed to fluctuate; the final number of water molecules is determined by the chemical potential. An unbiased sampling technique is used for the insertion/deletion procedure of the water molecules thereby providing a benchmark grand ensemble simulation of the hydration structure of proteins. Three different chemical potential simulations were carried out offering a direct route to thermodynamic information from a molecular dynamics simulation.