<div dir="ltr"><b id="m_-6643654875478223722m_469937116052285799gmail-docs-internal-guid-2a11739e-0f22-69c3-8731-99387df1932a" style="color:rgb(0,0,0);font-family:-webkit-standard;text-decoration:none;font-weight:normal"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">Hello GROMACS developers and power users.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">The Kasson Lab at the University of Virginia has recently published and released to beta the gmxapi framework, an API (but not just) to allow more flexible and extensible use of GROMACS. We would like to share our work and get your feedback on next steps, so I invite you to attend a “show-and-tell” of our current functionality, our API design, and our plans for deeper infrastructural integration with GROMACS.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">The paper can be accessed at:</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><a href="https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty484/5038467" style="text-decoration:none" target="_blank"><span style="font-size:11pt;font-family:Arial;color:rgb(17,85,204);background-color:transparent;font-weight:400;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap">https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty484/5038467</span></a></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">The web-conference will be 1 hour the last week of June (25--29). Please fill out this Doodle poll to help us choose an exact date and time. You can indicate when you are or aren’t available as well as preferred times (“yes” versus “yes, if need be”).</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">Vote for date and time: </span><a href="https://doodle.com/poll/h8wu773nbp6btks6" style="text-decoration:none" target="_blank"><span style="font-size:11pt;font-family:Arial;color:rgb(17,85,204);background-color:transparent;font-weight:400;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;text-decoration:underline;vertical-align:baseline;white-space:pre-wrap">https://doodle.com/poll/h8wu773nbp6btks6</span></a></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">If you are interested in API access, Python interfaces for GROMACS installations, or have a stake in GROMACS architecture, we hope you will be able to join us for an hour to see what gmxapi does and to help us make it a useful and sustainable part of the GROMACS ecosystem.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">gmxapi currently consists of a Python package for scripting MD simulation, a framework (with example code) for extending GROMACS with external C++ code, and a GROMACS fork with modifications to support the higher-level API functionality. In the first beta release we demonstrate restrained-ensemble simulations with custom external forces and a Python script to drive the workflow.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">To move forward with the project, we need to contribute additional features and infrastructure to the core GROMACS software. Our intention is that GROMACS users should have access to GROMACS through a designed Python interface and stable C++ programming environment for future out-of-the-box GROMACS installations.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">Thank you for your time,</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">M. Eric Irrgang</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:400;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">Peter M. Kasson</span></p></b><br></div>