[Zephyr-news] OpenMM workshop registration now open

[Joy P. Ku]

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.  

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
<http://simtk.org/home/msmbuilder>  software[3] to automatically construct
Markov State Models for trajectory analysis. 

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 <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. (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.

 

 

 

_______________________________________________

 

Joy P. Ku, PhD

Director of Dissemination, Simbios

 <http://simbios.stanford.edu> http://simbios.stanford.edu

 

Director of Communications & Training,

National Center for Simulation in Rehabilitation Research

 <http://opensim.stanford.edu> http://opensim.stanford.edu

 

(W)  650.736.8434, (F)  650.723.7461

Email:   <mailto:joyku at stanford.edu> joyku at stanford.edu

 

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