[gmx-developers] Accurate energy minization is not reliable

[Erik Lindahl]

Hi,

... and it still works fine, at least in my hands ;-)

Details are available at https://redmine.gromacs.org/issues/2641, 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.

Cheers,

Erik


On Wed, Sep 12, 2018 at 7:34 AM Bert de Groot <bgroot at gwdg.de> wrote:

> 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
> >     --
> >     Gromacs Developers mailing list
> >
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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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-- 
Erik Lindahl <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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