Background and Motivation¶

Conformation Dynamics with MSMBuilder¶

This slide deck gives an introduction to the MSMBuilder package and the design of its Python API. The code for the slides can be copied from the file slides.md found here.

The goals¶

The aim of this package is to provide software tools for predictive modeling of the long timescale dynamics of biomolecular systems using statistical modeling to analyze physical simulations.

The basic question we’re interested in is, “given a dataset of one or more stochastic trajectories tracking the coordinates of every (>10,000+) atom in a molecular system at a discrete time interval, how do we understand the slow dynamical processes and make quantitative predictions about the system?”

Workflow¶

1. Set up a system for molecular dynamics, and run one or more simulations for as long as you can on as many CPUs or GPUs as you have access to.

• There are a lot of great software packages for running MD, e.g OpenMM, Gromacs, Amber, CHARMM, and many others. MSMBuilder is not one of them.

2. Analyze your simulations with MSMBuilder.

• Build estimators for the long-timescale dynamical processes
• Perform model selection using cross-validation with the generalized matrix Rayleigh quotient.

3. Profit.