[gmx-developers] Accurate energy minization is not reliable

[Bert de Groot]

Hi,

In the gromacs 3 days CG was sufficient (many thousands of steps) but would 
require double precision for NMA.

cheers

Bert

On 09/11/18 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
> 
>