<HTML><BODY><div style="font-family: Arial, Tahoma, Verdana, sans-serif;" data-mce-style="font-family: Arial, Tahoma, Verdana, sans-serif;">Dear David!</div><div style="font-family: Arial, Tahoma, Verdana, sans-serif;" data-mce-style="font-family: Arial, Tahoma, Verdana, sans-serif;">thank you for your letter,</div><div style="font-family: Arial, Tahoma, Verdana, sans-serif;" data-mce-style="font-family: Arial, Tahoma, Verdana, sans-serif;">could you give me some references <span style="font-family: arial, tahoma, verdana, sans-serif;" data-mce-style="font-family: arial, tahoma, verdana, sans-serif;">of incremental clustering </span><span style="font-family: arial, tahoma, verdana, sans-serif;" data-mce-style="font-family: arial, tahoma, verdana, sans-serif;">algorithm </span>to start with?</div><div style="font-family: Arial, Tahoma, Verdana, sans-serif;" data-mce-style="font-family: Arial, Tahoma, Verdana, sans-serif;">Thank you in advance,</div><div style="font-family: Arial, Tahoma, Verdana, sans-serif;" data-mce-style="font-family: Arial, Tahoma, Verdana, sans-serif;">sincerely yours, <br>Boris Timofeev</div><br><br><br><blockquote style="border-left:1px solid #0857A6; margin:10px; padding:0 0 0 10px;">
Воскресенье, 5 августа 2018, 23:46 +03:00 от David van der Spoel <spoel@xray.bmc.uu.se>:<br>
<br>
<div id="">
<div class="js-helper js-readmsg-msg">
<style type="text/css"></style>
<div>
<base target="_self" href="https://e.mail.ru/">
<div id="style_15335019940000000172_BODY">Den 2018-08-04 kl. 23:00, skrev Boris Timofeev:<br>
> Dear David!<br>
> <br>
> Option -dr, it is new?<br>
> Perhaps, you meant - dt? There is no wish to thin out a trajectory.<br>
-dt indeed. The reason for long simulations is typically that <br>
transitions are slow and that it take long time to equilibrate. That <br>
also means that frames near each other are highly correlated and <br>
therefore the -dt option is no problem. However, this is obviously <br>
problem dependent.<br>
<br>
It could be possible to devise some kind of incremental clustering <br>
algorithm that stores cluster centers and dynamically updates them. In <br>
that manner the whole trajectory does not need to be stored. However <br>
that would be a research project in itself, and I guess this kind of <br>
algorithms has been developed long time ago. If you find such an <br>
algorithm you could consider implementing it. Alternatively, if you see <br>
a way of getting around the N^2 RMSD matrix in the existing algorithms <br>
that would be interesting too.<br>
<br>
> Sincerely,<br>
> Boris.<br>
> <br>
> <br>
> Суббота, 4 августа 2018, 16:09 +03:00 от David van der Spoel<br>
> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>:<br>
> <br>
> Den 2018-07-26 kl. 14:02, skrev Boris Timofeev:<br>
> > Dear developers!<br>
> ><br>
> > The existing realization of "gmx cluster" for calculations uses<br>
> > RMSD-matrix,<br>
> > quadratically increasing with increase in length of a trajectory,<br>
> > and already since 20000 frames calculation of clusters becomes<br>
> impossible<br>
> > because of requirements to memory and time.<br>
> ><br>
> > Whether there are some special methods for a clustering of<br>
> trajectories<br>
> > of big duration,<br>
> > containing 100000 and more frames?<br>
> Use the -dr flag.<br>
> ><br>
> > Best wishes<br>
> > Boris Timofeev.<br>
> ><br>
> ><br>
> ><br>
> ><br>
> ><br>
> <br>
> <br>
> -- <br>
> David van der Spoel, Ph.D., Professor of Biology<br>
> Head of Department, Cell & Molecular Biology, Uppsala University.<br>
> Box 596, SE-75124 Uppsala, Sweden. Phone: <span class="js-phone-number">+46184714205</span>.<br>
> <a href="http://www.icm.uu.se" target="_blank">http://www.icm.uu.se</a><br>
> -- <br>
> Gromacs Developers mailing list<br>
> <br>
> * Please search the archive at<br>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a><br>
> before posting!<br>
> <br>
> * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
> <br>
> * For (un)subscribe requests visit<br>
> <a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a><br>
> or send a mail to gmx-developers-request@gromacs.org.<br>
> <br>
> <br>
> <br>
> -- <br>
> Boris Timofeev<br>
> <br>
> <br>
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Head of Department, Cell & Molecular Biology, Uppsala University.<br>
Box 596, SE-75124 Uppsala, Sweden. Phone: <span class="js-phone-number">+46184714205</span>.<br>
<a href="http://www.icm.uu.se" target="_blank">http://www.icm.uu.se</a><br>
-- <br>
Gromacs Developers mailing list<br>
<br>
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!<br>
<br>
* Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
* For (un)subscribe requests visit<br>
<a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to gmx-developers-request@gromacs.org.</div>
<base target="_self" href="https://e.mail.ru/">
</div>
</div>
</div>
</blockquote>
<br>
<br>-- <br>Boris Timofeev<br></BODY></HTML>