Software

MSMBuilder

MSMBuilder is a python package which implements a series of statistical models for high-dimensional time-series.

It is particularly focused on the analysis of atomistic simulations of biomolecular dynamics. For example, MSMBuilder has been used to model protein folding and conformational change from molecular dynamics (MD) simulations.

FAHBench

FAHBench is a GPU benchmarking tool based on OpenMM and molecular dynamics.

Folding@Home donors test and report scores for GPUs to find the best performance for a given price.

MDTraj

MDTraj is a python library that allows researchers to read, write and analyze any of the dazzling array of MD formats in common use.

Wetmsm

wetmsm functions as a plugin for MSMBuilder. It implements the “solvent shells” metric for investigating water, lipids, and other solvents in the MSM framework.