<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hi Peter,
<div class=""><br class="">
</div>
<div class="">Thanks for the pointer. It seems like this could work, but the forces calculated by my restraint do not always decompose into pairs of atoms. Some of the forces depend on the positions of up to six hydrogen atoms at once.</div>
<div class=""><br class="">
</div>
<div class="">As far as I can tell, there’s no way through the API as implemented to get access the more than two atoms at a time. Perhaps there’s some way to use SessionResources to read more coordinates when RestraintPotential::update() gets called on the
master rank?</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class=""><br class="">
</div>
<div class="">Colin<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Feb 2, 2019, at 06:58, Peter Kasson <<a href="mailto:kasson@virginia.edu" class="">kasson@virginia.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">
<div class=""><span style="color:rgb(33,33,33);font-family:sans-serif;font-size:13px" class="">Hi Colin, </span></div>
<div dir="ltr" class=""><span style="color:rgb(33,33,33);font-family:sans-serif;font-size:13px" class=""> Take a look at the custom force plugins. These may not be efficient for </span><span style="color:rgb(33,33,33);font-family:sans-serif;font-size:13px" class="">most
of the hydrogens on a large protein (they were designed for relatively</span><span style="color:rgb(33,33,33);font-family:sans-serif;font-size:13px" class=""> sparse restraints), but they should at least get you started. </span></div>
<div dir="ltr" class=""><span style="color:rgb(33,33,33);font-family:sans-serif;font-size:13px" class=""><br class="">
</span></div>
<div dir="ltr" class=""><span style="color:rgb(33,33,33);font-family:sans-serif;font-size:13px" class="">API for doing this: </span><a href="https://doi.org/10.1093/bioinformatics/bty484" rel="noreferrer" target="_blank" style="color:rgb(126,87,194);font-family:sans-serif;font-size:13px" class="">https://doi.org/10.1093/bioinformatics/bty484</a><br style="color:rgb(33,33,33);font-family:sans-serif;font-size:13px" class="">
<span style="color:rgb(33,33,33);font-family:sans-serif;font-size:13px" class="">Application to ensemble-averaged restraints for DEER:</span><br style="color:rgb(33,33,33);font-family:sans-serif;font-size:13px" class="">
<a href="https://doi.org/10.1002/anie.201810462" rel="noreferrer" target="_blank" style="color:rgb(126,87,194);font-family:sans-serif;font-size:13px" class="">https://doi.org/10.1002/anie.201810462</a><br style="color:rgb(33,33,33);font-family:sans-serif;font-size:13px" class="">
<span style="color:rgb(33,33,33);font-family:sans-serif;font-size:13px" class=""><br class="">
</span></div>
<div dir="ltr" class=""><span style="color:rgb(33,33,33);font-family:sans-serif;font-size:13px" class="">Best,</span><br style="color:rgb(33,33,33);font-family:sans-serif;font-size:13px" class="">
<span style="color:rgb(33,33,33);font-family:sans-serif;font-size:13px" class="">--Peter<br clear="all" class="">
<div class="">
<div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class=""><br class="">
----------------------------------------------------------------------<br class="">
Peter Kasson, MD, PhD<br class="">
Associate Professor<br class="">
Departments of Molecular Physiology and Biological Physics<br class="">
and of Biomedical Engineering<br class="">
University of Virginia<br class="">
</div>
</div>
</div>
</div>
</div>
</div>
</span><br class="">
</div>
</div>
-- <br class="">
Gromacs Developers mailing list<br class="">
<br class="">
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" class="">
http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!<br class="">
<br class="">
* Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" class="">
http://www.gromacs.org/Support/Mailing_Lists</a><br class="">
<br class="">
* For (un)subscribe requests visit<br class="">
<a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" class="">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to
<a href="mailto:gmx-developers-request@gromacs.org" class="">gmx-developers-request@gromacs.org</a>.</div>
</blockquote>
</div>
<br class="">
</div>
</body>
</html>