[gmx-users] grompp with cg does have problem!

[David Mobley]

Part of the reason I even ever tried CG is that I occasionally have problems
with L-BFGS (i.e. it stops after zero steps and says it's done) and I need
to use another minimization method. But I guess rather than complaining
about CG I should submit a Bugzilla so you can reproduce my problems with
L-BFGS. :) I'll try to get my act together and do this soon.

Thanks,
David


On 12/16/05, Erik Lindahl <lindahl at sbc.su.se> wrote:
>
> Hi,
>
> Mark is mostly right - the main reason is that we simply haven't
> found it worth the effort yet :-)
>
> The underlying problem is that minimization is really sensitive to
> tiny differences in coordinates, and even conservative constraint
> algorithms usually leave constraint errors in the order of 1e-6. This
> can lead to really strange artifacts since your system is no longer
> strictly conservative, so if you want really good minimization the
> best bet is to allow the molecule to be flexible and use e.g. BFGS.
>
> We're aware of it though, and will eventually add code to project out
> constraint forces with CG too, but for the above reason it's not a
> top priority!
>
> Cheers,
>
> Erik
>
>
> On Dec 16, 2005, at 11:42 PM, Mark Abraham wrote:
>
> > David Mobley wrote:
> >> Mark,
> >> It may well be the case that implicit water constraints are the
> >> problem, as the follow-up response seems to indicate (I haven't
> >> tried it myself). I guess I'd suggest that this be stated
> >> explicitly in the manual (and perhaps even in the section on input
> >> files which discusses options for minimizers, under the CG
> >> section, there should be a note saying that CG won't work with
> >> rigid water...).
> >
> > I filed a Bugzilla report for the same at http://
> > bugzilla.gromacs.org/show_bug.cgi?id=37
> >
> >> Also, perhaps this is naive, but CG works fine in AMBER without
> >> doing anything special. It might be worth checking there to see
> >> how AMBER handles this. Perhaps it is "properly" handling the
> >> water, and if so, GROMACS could do the same thing? Or perhaps it
> >> lets the water be flexible? I'm not sure, but it seems like the
> >> issue must already be one people have dealt with in these other
> >> packages.
> >
> > It's probably just that constraints aren't implemented in the
> > gromacs CG algorithm. It's probably not worth implementing either,
> > given that constraints can be used with steepest descent and L-BFGS.
> >
> > Mark
> > _______________________________________________
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> -----------------------------------------------------------
> Erik Lindahl  <lindahl at sbc.su.se>     Backup address:
> <erik.lindahl at gmail.com>
> Assistant Professor, Computational Structural Biology
> Stockholm Bioinformatics Center, Stockholm University, SE 106 91
> Stockholm
> Phone: +46 8 5537 8564     Fax: +46 8 5537 8214
>
>
>
>
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