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University of Connecticut School of Engineering Vi Q. Ha

MD-R - Molecular Dynamics library for Repast

The MD-R toolkit provides a three-dimensional continuous space projection and a large set of short-range molecular dynamics (MD) tools for Repast HPC.

The 3D projection gives Repast HPC the ability to simulate agents in three dimensional Cartesian space and it manages all MPI operations for parallel computing. The MD-R toolkit utilizes the provided 3D space projection to run short-range Molecular Dynamics simulations. It includes integration algorithms, thermostats, and potential functions for interacting agents. MD-R was designed to be intuitive and user friendly. Users are not required to have advanced knowledge of MD to create a simulation with MD-R. The toolkit automatically handles all major MD operations such as initiation, recording of MD parameters, creation of cell lists and neighbor lists containing the agents. It also determines when the agents need to be synchronized and applies thermodynamic constrains.

Three-dimensional continuous space projection for Repast

Molecular Dynamics library for Repast