CCL: Molecular Dynamics Workshop Series - Develop and Analyze Simulations

 Sent to CCL by: "Joy  Ku" [joyku=-=stanford.edu]
 Simbios is excited to announce its upcoming Molecular Dynamics (MD) Workshop
 Series, highlighting new capabilities within the recently released OpenMM 3.0,
 including its Python API and integration of the AMOEBA polarizable force field
 with OpenMM.
 OpenMM is a freely downloadable library that enables MD simulations to run on
 high performance computer architectures. It has demonstrated speed ups for both
 implicit solvent[1] and explicit solvent simulations[2] on GPUs.
 WHERE:  Stanford University
 WHEN:  May 23-24, 2011  (sign up for one or two days)
 DAY 1:   DEVELOPING MOLECULAR DYNAMICS ON GPUS WITH OPENMM
 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.
 DAY 2:   INTRODUCTION TO MOLECULAR DYNAMICS AND TRAJECTORY ANALYSIS WITH MARKOV
 STATE MODELS
 For researchers (including novices to MD) interested in using MD and/or
 analyzing MD results in their research.   Deepen your knowledge about MD
 simulations and gain hands-on experience with using the MSMBuilder software[3]
 to automatically construct Markov State Models for trajectory analysis.
 REGISTRATION:  Registration is free but required and spaces are limited. To
 register or for more information, visit http://simbios.stanford.edu/MDWorkshops.htm.
 ________________________________________
 OpenMM and MSMBuilder are supported by Simbios, an NIH National Center for
 Physics-Based Simulation of Biological Structures. To learn more about Simbios
 and its research and software tools, visit http://simbios.stanford.edu.
 [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.
 [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.