[Simbiosnews] Announcing Molecular Dynamics Workshop Series in June

[Joy P. Ku]

Simbios would like to invite you to our upcoming Molecular Dynamics
Workshop Series.  The series consists of three workshops, showcasing
software designed for individuals with different interests and experience
with MD, from novices to experts.  Details are below.  

 

We'd appreciate you forwarding this announcement on to others that may be
interested in attending.  Thank you.

 

Regards,

Joy

 

_____________________________________________________

 

The Molecular Dynamics Workshop Series 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.
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.  

 

When:  

OpenMM Developers Workshop - June 24, 2009 

(additional days for integration of OpenMM - June 25-26, 2009) 

Introduction to Markov State Models and MSMBuilder - June 25, 2009

Introduction to Molecular Dynamics & OpenMM Zephyr - June 26, 2009

             

Where:  Stanford University. 

 

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.

 

 

______________________________________________________

 

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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