Molecular Dynamics Workshop Series, June 24-26, 2009
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Day 1 -- OpenMM
Geared towards developers who are interested in using the OpenMM library to enable their MD code to run on high performance computer architectures, such as GPUs. The current version of the freely downloadable OpenMM enables MD codes to run on NVIDIA and ATI GPUs, and has demonstrated speed ups of over 100X for implicit solvent simulations.[1]
Meeting Materials
Jun 24, 2009

  

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[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. (2009)


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Day 2 -- MSMBuilder
For researchers who want to analyze MD simulations, mapping out the metastable states of a molecule and the transition rates between them. You will learn about Markov State Models and why they are suitable for this, and use the MSMBuilder software[2] to automatically construct such models, as well as analyze and visualize them.
Workshop Materials
Jun 25, 2009

  

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[2] GR Bowman, X Huang, and VS Pande, "Using generalized ensemble simulations and Markov state models to identify conformational states," Methods (accepted). (2009)


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Day 3 -- MD & Zephyr
For researchers interested in using MD in their research, including novices to MD. You will learn the theory behind MD and 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.
Workshop Materials
Jun 26, 2009

  

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Jul 09, 2009

  


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