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\paragraph{Simulation \subsection*{Simulation  Software (Table~\ref{mdtable})} Campari \cite{Vitalis_2009} conducts flexible Monte Carlo sampling of biopolymers in internal coordinate space, with built-in analysis routines to estimate structural properties and support for replica exchange and Wang-Landau sampling. 
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ProtoMol \cite{Matthey_2004}, and the associated MDLab Python bindings \cite{Cickovski_2009}, provides an object-oriented framework for prototyping algorithms for molecular dynamics simulations and includes an interface to OpenMM.  ProtoMS \cite{Michel_2006} is a Monte Carlo biomolecular simulation program which can be used to calculate relative and absolute free energies and water placement with the  GCMC and JAWS methodology. methodologies.  Sire is a collection of modular libraries intended to facilitate fast prototyping and the development of new algorithms for molecular simulation and molecular design. It has apps for system setup, simulation, and analysis.  yank is built off of OpenMM and provides a  Python interface for performing alchemical free energy calculations. \paragraph{Simulation \subsection*{Simulation  Setup and Analysis (Table~\ref{mdanalysis})} LOOS (Lightweight Object-Oriented Structure library) \cite{Romo_2014} is a C++ library (with Python bindings) for reading and analyzing molecular dynamics trajectories that also includes a number of standaloneanalysis  programs. lsfitpar \cite{Vanommeslaeghe_2015} derives bonded parameters for Class I force fields by performing a robust fit to potential energy scans provided by the user.