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<div class="moz-cite-prefix">Hi,<br>
<br>
Over the years I have heard complaints about the GROMACS energy
minimizers, CG and/or L-BFGS. Apparently they can be improved, but
I don't know how.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2018-09-11 11:47, Erik Lindahl wrote:<br>
</div>
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cite="mid:CAEJJM8He_Abz0oVq7nyq98RorCkn7HZUcZ2qZ4itNvpveO67aQ@mail.gmail.com">
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<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"
moz-do-not-send="true">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" moz-do-not-send="true">http://www.icm.uu.se</a><br>
-- <br>
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</blockquote>
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<div><br>
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-- <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" moz-do-not-send="true">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>
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