From owner-chemistry \\at// ccl.net Fri Apr 22 02:49:00 2011
From: "Joy Ku joyku]![stanford.edu" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: Molecular Dynamics Workshop Series - Develop and Analyze Simulations
Message-Id: <-44455-110422024604-17226-MmidQXK+hcnisbdZze8wDg ~~ server.ccl.net>
X-Original-From: "Joy  Ku" <joyku!^!stanford.edu>
Date: Fri, 22 Apr 2011 02:46:02 -0400


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.