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

[Szilárd Páll]

The thermostat choice is an easy example where there is a clear case to be
made for the proposed mdp option, but what other uses are these for such an
option? Unless there are at least a few, I'd say it's better to improve the
UI messages, option documentation, manual, etc. than introduce a ~
single-use option than to force users to set an option that may not even be
relevant (e.g. equilibration is simply chopped of with -b).

--
Szilárd


On Fri, Aug 24, 2018 at 3:36 PM Paul bauer <paul.bauer.q at gmail.com> wrote:

> To add my 2 cents to the discussion, I think having the explicit switch
> between preparation and production runs will be definitely useful for
> users, and I think it will also make it easier to rework the input
> settings if we can simply have one check at the beginning that
> determines if we are harsh in denying the use of options or not. As an
> additional bonus, I think mdrun could decide based on this setting if it
> is more bold in stating if options are wrong or not, something that gets
> lost when people just default to use maxwarn as an option for grompp to
> make errors go away.
>
> Cheers
>
> Paul
>
> On 24/08/2018 15:26, Justin Lemkul wrote:
> >
> >
> > On 8/24/18 9:09 AM, Mark Abraham wrote:
> >> Hi,
> >>
> >> 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.
> >
> > I also think there's value in having a user go into an .mdp file and
> > set "stage = preparation" because now they (presumably) know that what
> > they are doing is applying an algorithm that is intended for a
> > preparatory process. If we require a user to simply add -maxwarn 1 to
> > their grompp command, the user begins to think "yeah, that's how I can
> > make that error go away." The former requires scientific thought, the
> > latter emboldens carelessness.
> >
> > For those wondering the backstory, I started a Redmine at
> > https://redmine.gromacs.org/issues/2622 because I felt we were a bit
> > harsh in making the use of Berendsen a warning, because we also
> > caution users against using Parrinello-Rahman for equilibration. So if
> > one shouldn't use Parrinello-Rahman and *can't* use Berendsen, what
> > conclusion is the user to make about performing equilibration? In this
> > case, it's acceptable to use Berendsen, if and only if the user
> > acknowledges that the resulting ensembles are wrong and therefore
> > should not be collected as real data.
> >
> > -Justin
> >
> >> Mark
> >>
> >> On Fri, Aug 24, 2018 at 2:48 PM Victor Rosas Garcia
> >> <rosas.victor at gmail.com>
> >> wrote:
> >>
> >>> 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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