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OpenMM \cite{Eastman_2013} is a substantial toolkit for high performance molecular dynamics simulations that includes support for GPU acceleration.  PDB2PQR \cite{Dolinsky_2004} \cite{Dolinsky_2007}  prepares structures for electrostatics calculations by adding hydrogens, calculating sidechain pKa, adding missing heavy atoms, and assigning force field-dependent parameters; users can specify an ambient pH. PLUMED \cite{Tribello_2014} interfaces with an assortment of molecular dynamics software packages to provide a unified interface for performing free energy calculations using methods such as metadynamics, umbrella sampling and steered MD (Jarzynski).