<div dir="ltr">Hi,<div><br></div><div>I do strongly encourage everybody to try to attend. This infrastructure has the chance to provide lots of opportunity for innovation, while resolving several pain points, so it's important that we get your input and feedback, now that there are working examples, and before we commit too heavily to infrastructure choices.</div><div><br></div><div>I'l be at ISC that week, but I'll see you there!</div><div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Jun 20, 2018 at 6:36 PM Eric Irrgang <<a href="mailto:ericirrgang@gmail.com">ericirrgang@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello!<br>
<br>
I will be hosting a 1-hour "show-and-tell" video conference on Monday,<br>
25 June, at 17:00 Stockholm time, 8:00am U.S. Pacific Standard Time.<br>
<br>
World Time Buddy link: <a href="http://bit.ly/2tlhWKc" rel="noreferrer" target="_blank">http://bit.ly/2tlhWKc</a><br>
<br>
If you are interested in API access, Python interfaces for GROMACS<br>
installations, or have a stake in GROMACS architecture, we hope you<br>
will be able to join us for an hour to see what gmxapi does and to<br>
help us make it a useful and sustainable part of the GROMACS<br>
ecosystem.<br>
<br>
The Kasson Lab has recently published and released to beta the gmxapi<br>
framework, an API and tools to allow more flexible and extensible use<br>
of GROMACS. We would like to share our work and get your feedback on<br>
next steps, so I invite you to attend a “show-and-tell” of our current<br>
functionality, our API design, and our plans for deeper<br>
infrastructural integration with GROMACS.<br>
<br>
The paper can be accessed at:<br>
<a href="https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty484/5038467" rel="noreferrer" target="_blank">https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty484/5038467</a><br>
<br>
gmxapi currently consists of a Python package for scripting MD<br>
simulation, a framework (with example code) for extending GROMACS with<br>
external C++ code, and a GROMACS fork with modifications to support<br>
the higher-level API functionality. In the first beta release we<br>
demonstrate restrained-ensemble simulations with custom external<br>
forces and a Python script to drive the workflow.<br>
<br>
To move forward with the project, we need to contribute additional<br>
features and infrastructure to the core GROMACS software. Our<br>
intention is that GROMACS users should have access to GROMACS through<br>
a designed Python interface and stable C++ programming environment for<br>
future out-of-the-box GROMACS installations.<br>
<br>
On Monday, I hope I can illustrate the utility and practicality of our<br>
design and beta implementation, and to get feedback about the highest<br>
priority features or use cases for the most likely users. I also hope<br>
to clarify the big picture design philosophy and requirements in<br>
advance of proposed GROMACS integration.<br>
<br>
I will follow up with a link to the conference call.<br>
<br>
Best,<br>
M. Eric Irrgang<br>
-- <br>
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