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

Paul bauer paul.bauer.q at gmail.com
Fri Aug 24 15:35:47 CEST 2018

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.



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?  
>>> 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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