<div dir="ltr"><div dir="ltr">Hi,<div> </div>... and it still works fine, at least in my hands ;-)<div><br></div><div>Details are available at <a href="https://redmine.gromacs.org/issues/2641">https://redmine.gromacs.org/issues/2641</a>, but in this case I think it was a matter of using shifted interactions - I suspect the discontinuity in the force does not work well with minimization.<br></div><div><br></div><div>Cheers,</div><div><br></div><div>Erik</div><div><br></div><div><br><div class="gmail_quote"><div dir="ltr">On Wed, Sep 12, 2018 at 7:34 AM Bert de Groot <<a href="mailto:bgroot@gwdg.de" target="_blank">bgroot@gwdg.de</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">Hi,<br>
<br>
In the gromacs 3 days CG was sufficient (many thousands of steps) but would <br>
require double precision for NMA.<br>
<br>
cheers<br>
<br>
Bert<br>
<br>
On 09/11/18 11:47, Erik Lindahl wrote:<br>
> Hi,<br>
> <br>
> Not really a short-cut - it's a general recommendation for all CG and L-BFGS <br>
> algorithms (i.e., not specific to GROMACS) to run the outer iteration after a <br>
> few steps instead of the line minimizer, since that is much more efficient at <br>
> finding a good local minimum.<br>
> <br>
> If you have a concrete problem where it goes wrong put it on redmine and we can <br>
> try to have a look.<br>
> <br>
> Cheers,<br>
> <br>
> Erik<br>
> <br>
> On Tue, Sep 11, 2018 at 11:02 AM David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <br>
> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>> wrote:<br>
> <br>
> 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>
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> Erik Lindahl <<a href="mailto:erik.lindahl@dbb.su.se" target="_blank">erik.lindahl@dbb.su.se</a> <mailto:<a href="mailto:erik.lindahl@dbb.su.se" target="_blank">erik.lindahl@dbb.su.se</a>>><br>
> Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm University<br>
> Science for Life Laboratory, Box 1031, 17121 Solna, Sweden<br>
> <br>
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