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MSMBuilder \cite{Beauchamp_2011} is an application and Python library for building Markov models of high-dimensional trajectory data.  packmol \cite{Mart_nez_2009} is a utility for setting molecular systems by realistically packing molecules to obey a variety of constraints and can create solvent mixtures and lipid bilayers.  PDB2PQR \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).