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Provide workshop materials to introduce programmers and scientists to OpenMM and new features in version 3.0 (AMOEBA, Python API, serialization), as well as to MSMBuilder

Simbios is excited to announce its Molecular Dynamics Workshop Series:

Developing Molecular Dynamics (MD) on GPUs with OpenMM

This first day is intended for those interested in developing MD simulations on graphics processing units (GPUs) and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. A programming background is required. During the workshop, participants will:

  • 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 and explicit solvent simulations on GPUs.

  • Learn about new features in OpenMM 3.0, such as its Python API, its serialization capabilities, and the integration of the AMOEBA polarizable force field.

Introduction to Trajectory Analysis with Markov State Models

This workshop is intended for researchers analyzing MD results in their research. During the workshop, participants will:

  • 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 to automatically construct Markov State Models for trajectory analysis