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[1] and explicit solvent simulations[2] 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 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, participants will:
  
  
  • Acquire a deeper understanding of the theory behind MD
  • Be exposed to MD simulation applications, such as Zander, which reads AMBER/Sander input files and is able to accelerate molecular dynamics simulations on GPUs using the OpenMM libraries
  • 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
  Schedule
       May 23: Developing Molecular Dynamics on GPUs with OpenMM
       May 24: Introduction to MD and Trajectory Analysis with Markov State Models
  
  The agenda will be determined by participants' interests and backgrounds. A sample agenda is available here.

  Workshop Logistics

  The workshops will be held at Stanford University and are free to attend. However, registration is required and spaces are limited.

  Preparing for the Workshops

  For the workshop, attendees are expected to bring their own laptops with the necessary software already installed. Detailed instructions will be sent to participants before the workshops.
  

  Additional details (including directions, travel, & lodging info).
  

  
  [1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872.
  [2]Eastman, P. and Pande, V.S. (2009). Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit. Journal of Computational Chemistry. (In press)
  [3] GR Bowman, X Huang, and VS Pande, "Using generalized ensemble simulations and Markov state models to identify conformational states," Methods, 49(2):197-201.