MDLab: A molecular dynamics simulation prototyping environment

Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and ve- locities over a timestept. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep re- quired for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps. We present MDLab, a development environment for MD simu- lations built with Python which facilitates prototyping, testing, and debugging of these methods. MDLab provides constructs which allow the development of propa- gators, force calculators, and high level sampling protocols that run several instances of molecular dynamics. For computationally demanding sampling protocols which require testing on large biomolecules, MDL includes an interface to the OpenMM libraries of Friedrichs et al. which execute on graphical processing units (GPUs) and achieve considerable speedup over execution on the CPU. As an example of an interesting high level method developed in MDLab, we present a parallel imple- mentation of the On-The-Fly String Method of Maragliano and Vanden-Eijnden. MDLab is available at http://mdlab.sourceforge.net.