<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv=Content-Type content="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 12 (filtered medium)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.Section1
{page:Section1;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang=EN-US link=blue vlink=purple>
<div class=Section1>
<p class=MsoNormal>We would like to invite you to attend our next OpenMM
Developer’s workshop from June 24-26, 2009. It is part of our
Molecular Dynamics Workshop Series. See the announcement below for
details. <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>We’d appreciate you forwarding this to others that you
think may be interested in attending. Thank you.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Regards,<o:p></o:p></p>
<p class=MsoNormal>Joy<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><i><span style='font-size:10.0pt'>Joy P. Ku<o:p></o:p></span></i></p>
<p class=MsoNormal><i><span style='font-size:10.0pt'>Director of Dissemination<o:p></o:p></span></i></p>
<p class=MsoNormal><i><span style='font-size:10.0pt'>Simbios, Stanford
University<o:p></o:p></span></i></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>_____________________________________________________<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-autospace:none'><i><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'>Want to learn how to run molecular
dynamics (MD) simulations or analyze your results with Markov State Models? <o:p></o:p></span></i></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-autospace:none'><i><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'>Or are you an MD developer who wants to
know how to obtain 100X speedups of MD code on graphics processing units
(GPUs)?* <o:p></o:p></span></i></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-autospace:none'><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'><o:p> </o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-autospace:none'><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'>Whatever your MD interest, the free
upcoming Molecular Dynamics Workshop Series promises to be an exciting,
knowledge-filled opportunity. The series consists of three workshops,
showcasing software designed for individuals with different interests and
experience with MD, from novices to experts. <o:p></o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:40.5pt;text-autospace:none'><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'><o:p> </o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:40.5pt;text-autospace:none'><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'>The<b> OpenMM Developers Workshop </b>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. <b><o:p></o:p></b></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:40.5pt;text-autospace:none'><b><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'><o:p> </o:p></span></b></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:40.5pt;text-autospace:none'><b><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'>Introduction to Molecular Dynamics and
OpenMM Zephyr </span></b><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>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. <o:p></o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:40.5pt;text-autospace:none'><b><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'><o:p> </o:p></span></b></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:40.5pt;text-autospace:none'><b><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'>Introduction to Markov State Models and
MSMBuilder </span></b><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>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.<b> <o:p></o:p></b></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-autospace:none'><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'><o:p> </o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-autospace:none'><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'>When: <o:p></o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-indent:.5in;text-autospace:none'><span
style='font-size:12.0pt;font-family:"Times New Roman","serif"'>OpenMM
Developers Workshop – June 24, 2009 <o:p></o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:.5in;text-indent:.5in;text-autospace:none'><span
style='font-size:12.0pt;font-family:"Times New Roman","serif"'>(additional days
for integration of OpenMM – June 25-26, 2009) <o:p></o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-indent:.5in;text-autospace:none'><span
style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Introduction to
Markov State Models and MSMBuilder – June 25, 2009<o:p></o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-indent:.5in;text-autospace:none'><span
style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Introduction to
Molecular Dynamics & OpenMM Zephyr – June 26, 2009<o:p></o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-autospace:none'><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'> <o:p></o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-autospace:none'><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'>Where: Stanford University. <o:p></o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-autospace:none'><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'><o:p> </o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-autospace:none'><span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'>Registration is free but required and
spaces are limited. For more details, visit <a
href="http://simbios.stanford.edu/MDWorkshops.htm">http://simbios.stanford.edu/MDWorkshops.htm</a><o:p></o:p></span></p>
<div style='mso-element:para-border-div;border:none;border-bottom:solid windowtext 1.0pt;
padding:0in 0in 1.0pt 0in'>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-autospace:none;border:none;padding:0in'><span
style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p> </o:p></span></p>
</div>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-autospace:none'><span style='font-size:10.0pt;
font-family:"Times New Roman","serif"'>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. <o:p></o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-autospace:none'><span style='font-size:10.0pt;
font-family:"Times New Roman","serif"'><o:p> </o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:5.0pt;margin-right:0in;margin-bottom:
5.0pt;margin-left:0in;text-autospace:none'><span style='font-size:10.0pt;
font-family:"Times New Roman","serif"'>*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.<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
color:black'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal><o:p> </o:p></p>
</div>
</body>
</html>