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MDynaMix \cite{Lyubartsev_2000} is a basic general purpose molecular dynamics package.  MMTK (Molecular Modelling Toolkit) \cite{Hinsen_2000} is a library written in Python (with some time critical parts written in C) for constructing and simulating molecular systems. Its capabilities include molecular dynamics, energy minimization, and normal mode analysis. analysis and it is well-suited for methods development.  OpenMM \cite{Eastman_2013} is a substantial toolkit for high performance molecular dynamics simulations that includes support for GPU acceleration.