<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)"><!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>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. <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'><b><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Where:</span></b><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'> 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'><b><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>When:</span></b><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'> May 23-24, 2011 (sign up for one or two days)<o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><b><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Day 1:</span></b><b><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Developing Molecular Dynamics on GPUs with OpenMM<o:p></o:p></span></b></p><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>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. </span><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'><b><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Day 2:</span></b><b><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Introduction to Molecular Dynamics and Trajectory Analysis with Markov State Models </span></b><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:auto;margin-bottom:12.0pt'><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>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 <a href="http://simtk.org/home/msmbuilder">MSMBuilder</a> software[3] to automatically construct Markov State Models for trajectory analysis. <o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Registration is free but required and spaces are limited. To register or for more information, visit <a href="http://simbios.stanford.edu/MDWorkshops.htm">http://simbios.stanford.edu/MDWorkshops.htm</a>.<o:p></o:p></span></p><div class=MsoNormal align=center style='text-align:center'><b><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><hr size=2 width="100%" align=center></span></b></div><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"'>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 <a href="http://simbios.stanford.edu/">http://simbios.stanford.edu</a>. <o:p></o:p></span></i></p><p class=MsoNormal style='text-autospace:none'><o:p> </o:p></p><p class=MsoNormal><i><span style='font-size:6.0pt;font-family:"Verdana","sans-serif"'>[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.<br>[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)<br>[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.<o:p></o:p></span></i></p><p class=MsoNormal><i><span style='font-size:6.0pt;font-family:"Verdana","sans-serif"'><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><i><span style='font-size:10.0pt;color:#595959'>_______________________________________________<o:p></o:p></span></i></p><p class=MsoNormal><i><span style='font-size:10.0pt;color:#595959'><o:p> </o:p></span></i></p><p class=MsoNormal><i><span style='font-size:10.0pt;color:#595959'>Joy P. Ku, PhD<o:p></o:p></span></i></p><p class=MsoNormal><i><span style='font-size:10.0pt;color:#595959'>Director of Dissemination, Simbios<o:p></o:p></span></i></p><p class=MsoNormal><i><span style='font-size:10.0pt;color:#595959'><a href="http://simbios.stanford.edu"><span style='color:blue'>http://simbios.stanford.edu</span></a><o:p></o:p></span></i></p><p class=MsoNormal><i><span style='font-size:10.0pt;color:#595959'><o:p> </o:p></span></i></p><p class=MsoNormal><i><span style='font-size:10.0pt;color:#595959'>Director of Communications & Training,<o:p></o:p></span></i></p><p class=MsoNormal><i><span style='font-size:10.0pt;color:#595959'>National Center for Simulation in Rehabilitation Research<o:p></o:p></span></i></p><p class=MsoNormal><i><span style='font-size:10.0pt;color:#595959'><a href="http://opensim.stanford.edu"><span style='color:blue'>http://opensim.stanford.edu</span></a><o:p></o:p></span></i></p><p class=MsoNormal><i><span style='font-size:10.0pt;color:#595959'><o:p> </o:p></span></i></p><p class=MsoNormal><i><span style='font-size:10.0pt;color:#595959'>(W) 650.736.8434, (F) 650.723.7461<o:p></o:p></span></i></p><p class=MsoNormal><i><span style='font-size:10.0pt;color:#595959'>Email: <a href="mailto:joyku@stanford.edu"><span style='color:blue'>joyku@stanford.edu</span></a><o:p></o:p></span></i></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>