From owner-chemistry@ccl.net Thu May 14 13:27:01 2009 From: "Joy Ku joyku|-|stanford.edu" To: CCL Subject: CCL: Molecular Dynamics Workshop Series Message-Id: <-39326-090514124710-4749-bH8HZ1RoIm8ada2m5WEuvA\a/server.ccl.net> X-Original-From: "Joy Ku" Date: Thu, 14 May 2009 12:47:06 -0400 Sent to CCL by: "Joy Ku" [joyku::stanford.edu] When: * OpenMM Developers Workshop for speeding up your molecular dynamics code on GPUs June 24, 2009 (additional days for integration of OpenMM June 25-26, 2009) * Introduction to Markov State Models and MSMBuilder for analyzing molecular dynamics results June 25, 2009 * Introduction to Molecular Dynamics & OpenMM Zephyr June 26, 2009 Where: Stanford University === Details === The free upcoming Molecular Dynamics Workshop Series sponsored by Simbios, an NIH National Center for Biomedical Computing, consists of three workshops, showcasing software designed for individuals with different interests and experience with MD, from novices to experts. The OpenMM Developers Workshop is geared towards developers who are interested in using the OpenMM library to enable their MD code to run on high performance computer architectures. The current version of the freely downloadable OpenMM enables MD codes to run on NVIDIA and ATI GPUs and has shown 100X.* The workshop will highlight the explicit solvent capabilities that will be available in the next OpenMM release in June and include a special track focused on integration of OpenMM into AMBER. Introduction to Molecular Dynamics and OpenMM Zephyr is 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. Introduction to Markov State Models and MSMBuilder is for researchers who want to analyze the results of 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 to automatically construct such models, as well as analyze and visualize them. Registration is free but required and spaces are limited. For more details, visit http://simbios.stanford.edu/MDWorkshops.htm -------------------------------------------------------------------------- OpenMM, OpenMM Zephyr, and MSMBuilder are supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures, as part of its protein folding research efforts. To learn more about Simbios and its research and software tools, visit http://simbios.stanford.edu. *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.