<div dir="ltr">Hi,<div><br></div><div>Not really a short-cut - it's a general recommendation for all CG and L-BFGS algorithms (i.e., not specific to GROMACS) to run the outer iteration after a few steps instead of the line minimizer, since that is much more efficient at finding a good local minimum.</div><div><br></div><div>If you have a concrete problem where it goes wrong put it on redmine and we can try to have a look.</div><div><br></div><div>Cheers,</div><div><br></div><div>Erik </div></div><br><div class="gmail_quote"><div dir="ltr">On Tue, Sep 11, 2018 at 11:02 AM David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I am finding that energy minimization not always succeeds, even for very <br>
simple molecules such as 2-octanol or pentoxypentane. This leads to <br>
problems when you want to do a normal mode analysis based on that structure.<br>
<br>
The code for conjugate gradients has comments (from Erik) that suggest <br>
there are some short-cuts being taken (see example below). I do not want <br>
to modify this code, but it might be good to have a minimizer that <br>
*does* go all the way to zero force (steepest descents doesn't do it <br>
either).<br>
<br>
Suggestions?<br>
<br>
<br>
* In theory, we should minimize the function along this direction.<br>
* That is quite possible, but it turns out to take 5-10 <br>
function evaluations<br>
* for each line. However, we dont really need to find the <br>
exact minimum -<br>
* it is much better to start a new CG step in a modified <br>
direction as soon<br>
* as we are close to it. This will save a lot of energy <br>
evaluations.<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: +46184714205.<br>
<a href="http://www.icm.uu.se" rel="noreferrer" 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" rel="noreferrer" 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" rel="noreferrer" 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" rel="noreferrer" target="_blank">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" target="_blank">gmx-developers-request@gromacs.org</a>.<br>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>Erik Lindahl <<a href="mailto:erik.lindahl@dbb.su.se" target="_blank">erik.lindahl@dbb.su.se</a>></div><div>Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm University</div><div>Science for Life Laboratory, Box 1031, 17121 Solna, Sweden</div></div></div></div></div></div></div></div></div>