[Simbiosnews] Announcing Simbios' Molecular Dynamics Workshop Series - March 1-2

[Joy P. Ku]

Simbios is excited to announce its upcoming Molecular Dynamics (MD)
Workshop Series, highlighting new capabilities within the recently
released OpenMM 1.0 and introducing PyOpenMM for rapid MD code development
with high performance:

 

Day 1:  Running and Developing MD Algorithms on GPUs with OpenMM 

Day 2:   Introduction to MD and Trajectory Analysis with Markov State
Models 

 

When:  March 1-2, 2010  (sign up for one or two days)

Where:  Stanford University

 

Registration is free but required and spaces are limited. Visit
http://simbios.stanford.edu/MDWorkshops.htm.

  _____  

Day 1:  Running and Developing MD Algorithms 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. 

Learn to:

o    Set up simulations using OpenMM <http://simtk.org/home/openmm> , 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. 

o    Use OpenMM's custom force options to design and test new MD
algorithms 

o    Use PyOpenMM <http://simtk.org/home/pyopenmm> , the Python version of
OpenMM that is ideal for rapid code development but still achieves high
performance 

Day 2:  Introduction to MD 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. 

During the workshop, you will: 

o    Learn the theory behind MD 

o    Use the OpenMM Zephyr <http://simtk.org/home/zephyr>  application to
easily run and visualize MD simulations. OpenMM Zephyr incorporates the
OpenMM library, enabling acceleration of the simulations on GPUs. 

o    Learn different techniques for analyzing MD simulations, including
Markov State Models and why they are suitable for this 

o    Gain hands-on experience with the MSMBuilder
<http://simtk.org/home/msmbuilder>  software[3] to automatically construct
Markov State Models for trajectory analysis 

o     

OpenMM, OpenMM Zephyr, PyOpenMM, 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 <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

Director of Dissemination

Simbios, Stanford University

 

(W) 650.736.8434 

(F) 650.723.7461

Email:  joyku at stanford.edu

Website:  http://simbios.stanford.edu

 

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