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

Justin Lemkul jalemkul at vt.edu
Fri Aug 24 15:27:02 CEST 2018

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.


> 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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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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