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Etomica is a Java API and development environment for construction and implementation of molecular simulations. The API is a set of classes that can be employed to construct a molecular simulation in Java. Simulations may be constructed with them by programming in Java with a text editor, or by using the Etomica development environment. The development environment provides a graphical interface for constructing, running, and saving simulations based on the API. The Etomica environment provides for dynamic modification and interrogation of the simulation, while it is in progress.