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.

YANK

YANK is an open, extensible, GPU-accelerated platform for alchemical free energy calculations written in Python, making use of the powerful OpenMM simulation engine. 

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.

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.

repex

A flexible, extensible module for replica-exchange, parallel tempering, and Hamiltonian exchange using OpenMM.