Simbios is excited to announce its Molecular Dynamics Workshop Series. The series consists of two workshops. Materials from the workshops will be provided via this project.

Running and Developing Molecular Dynamics (MD) Algorithms on GPUs with OpenMM: The workshop is intended for those interested in running MD simulations on graphics processing units (GPUs) and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. Some programming background is required.

During the workshop, participants will learn to:

- Set up simulations using OpenMM, a freely downloadable library that enables MD simulations to run on high performance computer architectures. It has demonstrated significant speed ups for both implicit solvent[1] and explicit solvent simulations[2] on GPUs.

- Use OpenMM's custom force options to design and test new MD algorithms

- Use PyOpenMM, the Python version of OpenMM that is ideal for rapid code development but still achieves high performance

Introduction to Molecular Dynamics (MD) and Trajectory Analysis with Markov State Models: This workshop is intended for researchers (including novices to MD) interested in using MD and/or analyzing MD results in their research. During the workshop, you will:

- Learn the theory behind MD

- Use the OpenMM Zephyr application, which makes it easy to run and visualize MD simulations. OpenMM Zephyr incorporates the OpenMM library, enabling acceleration of the simulations on GPUs.

- Learn different techniques for analyzing MD simulations, including Markov State Models and why they are suitable for this

- Gain hands-on experience with the MSMBuilder software[3] to automatically construct Markov State Models for trajectory analysis.