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<pre>When: Monday, June 25, 2018 5:00 PM-6:00 PM. (UTC+01:00) Belgrade, Bratislava, Budapest, Ljubljana, Prague
Where: https://vconf.kth.se then type vroom_9301
*~*~*~*~*~*~*~*~*~*
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<p class="MsoNormal"><span style="font-family:'-webkit-standard',serif;color:black">Web browser: <a href="https://vconf.kth.se">https://vconf.kth.se</a> then type vroom_9301<o:p><br>
</o:p></span></p>
<p class="MsoNormal"><span style="font-family:'-webkit-standard',serif;color:black">SIP: vroom_9301 at vconf.kth.se<o:p><br>
</o:p></span></p>
<p class="MsoNormal"><span style="font-family:'-webkit-standard',serif;color:black">IP: 130.237.210.139 and choose room 9301<o:p><br>
</o:p></span></p>
<p class="MsoNormal"><span style="font-family:'-webkit-standard',serif;color:black">Telephone: + 46 8 790 6421 and choose room 9301<o:p><br>
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<p class="MsoNormal"><span style="font-family:'-webkit-standard',serif;color:black"><o:p><br>
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The paper can be accessed at:<o:p><br>
</o:p></span></p>
<p class="MsoNormal"><span style="font-family:'-webkit-standard',serif;color:black"><a href="https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty484/5038467">https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty484/5038467</a><o:p><br>
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<p class="MsoNormal"><span lang="EN-GB"><o:p><br>
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<p class="MsoNormal">On 20.06.18, 18:35, "Eric Irrgang" <<a href="mailto:ericirrgang@gmail.com">ericirrgang@gmail.com</a>> wrote:<o:p><br>
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<p class="MsoNormal"><o:p><br>
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<p class="MsoNormal"> Hello!<o:p><br>
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<p class="MsoNormal"> <o:p><br>
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<p class="MsoNormal"> I will be hosting a 1-hour "show-and-tell" video conference on Monday,<o:p><br>
</o:p></p>
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<p class="MsoNormal"> 25 June, at 17:00 Stockholm time, 8:00am U.S. Pacific Standard Time.<o:p><br>
</o:p></p>
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<p class="MsoNormal"> <o:p><br>
</o:p></p>
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<p class="MsoNormal"> World Time Buddy link: <a href="http://bit.ly/2tlhWKc">http://bit.ly/2tlhWKc</a><o:p><br>
</o:p></p>
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<p class="MsoNormal"> <o:p><br>
</o:p></p>
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<p class="MsoNormal"> If you are interested in API access, Python interfaces for GROMACS<o:p><br>
</o:p></p>
</div>
<div>
<p class="MsoNormal"> installations, or have a stake in GROMACS architecture, we hope you<o:p><br>
</o:p></p>
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<div>
<p class="MsoNormal"> will be able to join us for an hour to see what gmxapi does and to<o:p><br>
</o:p></p>
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<p class="MsoNormal"> help us make it a useful and sustainable part of the GROMACS<o:p><br>
</o:p></p>
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<div>
<p class="MsoNormal"> ecosystem.<o:p><br>
</o:p></p>
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<div>
<p class="MsoNormal"> <o:p><br>
</o:p></p>
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<p class="MsoNormal"> The Kasson Lab has recently published and released to beta the gmxapi<o:p><br>
</o:p></p>
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<div>
<p class="MsoNormal"> framework, an API and tools to allow more flexible and extensible use<o:p><br>
</o:p></p>
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<p class="MsoNormal"> of GROMACS. We would like to share our work and get your feedback on<o:p><br>
</o:p></p>
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<p class="MsoNormal"> next steps, so I invite you to attend a “show-and-tell” of our current<o:p><br>
</o:p></p>
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<p class="MsoNormal"> functionality, our API design, and our plans for deeper<o:p><br>
</o:p></p>
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<p class="MsoNormal"> infrastructural integration with GROMACS.<o:p><br>
</o:p></p>
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<p class="MsoNormal"> <o:p><br>
</o:p></p>
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<p class="MsoNormal"> The paper can be accessed at:<o:p><br>
</o:p></p>
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<div>
<p class="MsoNormal"> <a href="https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty484/5038467">https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty484/5038467</a><o:p><br>
</o:p></p>
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<div>
<p class="MsoNormal"> <o:p><br>
</o:p></p>
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<p class="MsoNormal"> gmxapi currently consists of a Python package for scripting MD<o:p><br>
</o:p></p>
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<p class="MsoNormal"> simulation, a framework (with example code) for extending GROMACS with<o:p><br>
</o:p></p>
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<p class="MsoNormal"> external C++ code, and a GROMACS fork with modifications to support<o:p><br>
</o:p></p>
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<p class="MsoNormal"> the higher-level API functionality. In the first beta release we<o:p><br>
</o:p></p>
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<p class="MsoNormal"> demonstrate restrained-ensemble simulations with custom external<o:p><br>
</o:p></p>
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<p class="MsoNormal"> forces and a Python script to drive the workflow.<o:p><br>
</o:p></p>
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<div>
<p class="MsoNormal"> <o:p><br>
</o:p></p>
</div>
<div>
<p class="MsoNormal"> To move forward with the project, we need to contribute additional<o:p><br>
</o:p></p>
</div>
<div>
<p class="MsoNormal"> features and infrastructure to the core GROMACS software. Our<o:p><br>
</o:p></p>
</div>
<div>
<p class="MsoNormal"> intention is that GROMACS users should have access to GROMACS through<o:p><br>
</o:p></p>
</div>
<div>
<p class="MsoNormal"> a designed Python interface and stable C++ programming environment for<o:p><br>
</o:p></p>
</div>
<div>
<p class="MsoNormal"> future out-of-the-box GROMACS installations.<o:p><br>
</o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p><br>
</o:p></p>
</div>
<div>
<p class="MsoNormal"> On Monday, I hope I can illustrate the utility and practicality of our<o:p><br>
</o:p></p>
</div>
<div>
<p class="MsoNormal"> design and beta implementation, and to get feedback about the highest<o:p><br>
</o:p></p>
</div>
<div>
<p class="MsoNormal"> priority features or use cases for the most likely users. I also hope<o:p><br>
</o:p></p>
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<p class="MsoNormal"> to clarify the big picture design philosophy and requirements in<o:p><br>
</o:p></p>
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<p class="MsoNormal"> advance of proposed GROMACS integration.<o:p><br>
</o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p><br>
</o:p></p>
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<div>
<p class="MsoNormal"> I will follow up with a link to the conference call.<o:p><br>
</o:p></p>
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<div>
<p class="MsoNormal"> <o:p><br>
</o:p></p>
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<div>
<p class="MsoNormal"> Best,<o:p><br>
</o:p></p>
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<div>
<p class="MsoNormal"> M. Eric Irrgang<o:p><br>
</o:p></p>
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<p class="MsoNormal"> <o:p><br>
</o:p></p>
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