<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<meta name="Generator" content="Microsoft Exchange Server">
<!-- converted from rtf -->
<style><!-- .EmailQuote { margin-left: 1pt; padding-left: 4pt; border-left: #800000 2px solid; } --></style>
</head>
<body>
<font face="Times New Roman" size="3"><span style="font-size:12pt;"><a name="BM_BEGIN"></a>
<div><font face="Courier New">When: Monday, June 25, 2018 5:00 PM-6:00 PM. (UTC+01:00) Belgrade, Bratislava, Budapest, Ljubljana, Prague<br>
Where: <a href="https://vconf.kth.se">https://vconf.kth.se</a> then type vroom_9301<br>
<br>
*~*~*~*~*~*~*~*~*~*<br>
</font></div>
<div><font face="-webkit-standard" size="2"><span style="font-size:11pt;">Web browser: <a href="https://vconf.kth.se"><font color="blue"><u>https://vconf.kth.se</u></font></a> then type vroom_9301<br>
</span></font></div>
<div><font face="-webkit-standard" size="2"><span style="font-size:11pt;">SIP: vroom_9301 at vconf.kth.se<br>
</span></font></div>
<div><font face="-webkit-standard" size="2"><span style="font-size:11pt;">IP: 130.237.210.139 and choose room 9301<br>
</span></font></div>
<div><font face="-webkit-standard" size="2"><span style="font-size:11pt;">Telephone: + 46 8 790 6421 and choose room 9301<br>
</span></font></div>
<div><br>
</div>
<div><br>
<font face="-webkit-standard" size="2"><span style="font-size:11pt;">The paper can be accessed at:<br>
</span></font></div>
<div><a href="https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty484/5038467"><font face="-webkit-standard" size="2" color="blue"><span style="font-size:11pt;"><u>https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty484/5038467</u></span></font></a><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;">On 20.06.18, 18:35, "Eric Irrgang" <<a href="mailto:ericirrgang@gmail.com"><font color="blue"><u>ericirrgang@gmail.com</u></font></a>> wrote:<br>
</span></font></div>
<div><br>
</div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> Hello!<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> <br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> I will be hosting a 1-hour "show-and-tell" video conference on Monday,<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> 25 June, at 17:00 Stockholm time, 8:00am U.S. Pacific Standard Time.<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> <br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> World Time Buddy link: <a href="http://bit.ly/2tlhWKc"><font color="blue"><u>http://bit.ly/2tlhWKc</u></font></a><br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> <br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> If you are interested in API access, Python interfaces for GROMACS<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> installations, or have a stake in GROMACS architecture, we hope you<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> will be able to join us for an hour to see what gmxapi does and to<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> help us make it a useful and sustainable part of the GROMACS<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> ecosystem.<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> <br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> The Kasson Lab has recently published and released to beta the gmxapi<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> framework, an API and tools to allow more flexible and extensible use<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> of GROMACS. We would like to share our work and get your feedback on<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> next steps, so I invite you to attend a “show-and-tell” of our current<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> functionality, our API design, and our plans for deeper<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> infrastructural integration with GROMACS.<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> <br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> The paper can be accessed at:<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> <a href="https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty484/5038467"><font color="blue"><u>https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty484/5038467</u></font></a><br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> <br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> gmxapi currently consists of a Python package for scripting MD<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> simulation, a framework (with example code) for extending GROMACS with<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> external C++ code, and a GROMACS fork with modifications to support<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> the higher-level API functionality. In the first beta release we<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> demonstrate restrained-ensemble simulations with custom external<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> forces and a Python script to drive the workflow.<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> <br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> To move forward with the project, we need to contribute additional<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> features and infrastructure to the core GROMACS software. Our<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> intention is that GROMACS users should have access to GROMACS through<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> a designed Python interface and stable C++ programming environment for<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> future out-of-the-box GROMACS installations.<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> <br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> On Monday, I hope I can illustrate the utility and practicality of our<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> design and beta implementation, and to get feedback about the highest<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> priority features or use cases for the most likely users. I also hope<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> to clarify the big picture design philosophy and requirements in<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> advance of proposed GROMACS integration.<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> <br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> I will follow up with a link to the conference call.<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> <br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> Best,<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> M. Eric Irrgang<br>
</span></font></div>
<div><font face="Calibri" size="2"><span style="font-size:11pt;"> <br>
</span></font></div>
</span></font>
</body>
</html>