[gmx-developers] Accurate energy minization is not reliable

[Berk Hess]

Hi,

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.

Cheers,

Berk

On 2018-09-11 11:47, Erik Lindahl wrote:
> Hi,
>
> 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.
>
> If you have a concrete problem where it goes wrong put it on redmine 
> and we can try to have a look.
>
> Cheers,
>
> Erik
>
> On Tue, Sep 11, 2018 at 11:02 AM David van der Spoel 
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>
>     Hi,
>
>     I am finding that energy minimization not always succeeds, even
>     for very
>     simple molecules such as 2-octanol or pentoxypentane. This leads to
>     problems when you want to do a normal mode analysis based on that
>     structure.
>
>     The code for conjugate gradients has comments (from Erik) that
>     suggest
>     there are some short-cuts being taken (see example below). I do
>     not want
>     to modify this code, but it might be good to have a minimizer that
>     *does* go all the way to zero force (steepest descents doesn't do it
>     either).
>
>     Suggestions?
>
>
>               * In theory, we should minimize the function along this
>     direction.
>               * That is quite possible, but it turns out to take 5-10
>     function evaluations
>               * for each line. However, we dont really need to find the
>     exact minimum -
>               * it is much better to start a new CG step in a modified
>     direction as soon
>               * as we are close to it. This will save a lot of energy
>     evaluations.
>               *
>
>
>     -- 
>     David van der Spoel, Ph.D., Professor of Biology
>     Head of Department, Cell & Molecular Biology, Uppsala University.
>     Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>     http://www.icm.uu.se
>     -- 
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>
>
> -- 
> Erik Lindahl <erik.lindahl at dbb.su.se <mailto:erik.lindahl at dbb.su.se>>
> Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm 
> University
> Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
>
>

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