Simulate.  Analyze.  Explore.  High performance, high usability toolkits for  predictive biomolecular simulation.

 

OpenMM

OpenMM is CPU / GPU accelerated molecular dynamics with an intuitive Python interface.  Wrappers for C, C++, and Fortran.

MDTraj

Easy-to-use trajectory readers for almost every simulation format imaginable.  Read, write, and analyze trajectories with only a few lines of Python code.

MSMBuilder

MSMBuilder creates kinetic rate models from multiple simulations.  Parallelizes the molecular simulation problem and enables direct comparison to experiment.

PDBFixer

A powerful, flexible tool for preparing PDB files for molecular simulation or modeling, capable of running in interactive, Python-scriptable, or fully automated modes.

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