[gmx-users] Feedback wanted - mdp option for preparation vs production

Mark Abraham mark.j.abraham at gmail.com
Fri Aug 24 15:10:08 CEST 2018


You can't prevent misuse... give someone a scalpel and they might lose a
finger! The key targets for helping are the newer users who don't have the
experience to know which way to hold the scalpel. If they can be trained to
use these flags (e.g. because they see them in their tutorials) then the
warnings can have the intended effect. One can mitigate the impact of
someone always running in the least safe mode by reporting on that to the
log file, so that they'll see it, and so will their collaborators, or their
peers when they archive and share their results.


On Fri, Aug 24, 2018 at 2:48 PM Victor Rosas Garcia <rosas.victor at gmail.com>

> El jue., 23 ago. 2018 a las 17:03, Mark Abraham (<mark.j.abraham at gmail.com
> >)
> escribió:
> > Hi,
> >
> > [snip, snip]
> > Despite this, there are times when one might want to use such an
> algorithm,
> > and so we permit users to suppress warnings from grompp with -maxwarn.
> > However, encouraging such behaviour leads to people abusing -maxwarn, and
> > we'd all like to avoid that.
> >
> > [snip, snip]
> > Following discussion among some developers, how do people feel about a
> new
> > mdp option that permits users to specify e.g. "production" or
> > "preparation," defaulting to "production." grompp retains its current
> > warning behaviour for "production," but merely advises about such issues
> > when preparing systems. Do those names and behaviours seem suitable? Do
> we
> > need more flavours of calculation type?
> >
> > Hello Mark,
> First of all, thanks for all the time and effort you put into these
> matters.
> Regarding these new flavours of calculation, how will these new flavours
> prevent abuse?  If people are abusing -maxwarn, what will keep these same
> people from using always "preparation" to suppress the warnings?  GROMACS
> is a great program but in the end, it boils down to the fundamental
> question "do you want to do a good job or a bad job?" I'm all for getting
> clearer error messages and more complete warnings (sometimes I have learned
> from them).
> just my 2 cents
> Victor
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