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

Mark Abraham mark.j.abraham at gmail.com
Fri Aug 24 17:01:47 CEST 2018


On Fri, Aug 24, 2018 at 4:55 PM Szilárd Páll <pall.szilard at gmail.com> wrote:

> On Fri, Aug 24, 2018 at 4:23 PM Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> > Hi,
> > the
> > There's other examples, e.g. freeze groups, pressure coupling with
> position
> > restraints, maybe position restraints generally, generating velocities,
> > size of steps, time constants of coupling algorithms. Obviously we can
> > always improve docs and messages, but equally users aren't always going
> to
> > read them. :-)
> >
> > How does the consideration of needing to discard a fraction of a
> production
> > run (e.g. with trjconv -b) matter?.
> That for some users/use-cases there may not be much difference between
> (part of) the "preparation" stage and the "production" stage and therefore,
> unless the user remembers to change the mdp option, they will get warnings
> that will end up ignored.

What's a concrete example where a user who isn't over-using maxwarn has a
new problem?

> BTW, is it part of the proposal to make warnings fatal and remove -maxwarn,
> i.e. require the user to eliminate certain/all warning through means?

No, or I'd have written that ;-) One might want to demonstrate the
artefacts, or replicate old results with such methods, so the
implementations remain useful to have available somehow.


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