[gmx-developers] functionality to deprecate in 2018 release

Justin Lemkul jalemkul at vt.edu
Thu Jan 4 14:43:08 CET 2018

On 1/4/18 4:55 AM, Mark Abraham wrote:
> Hi,
> On Thu, Jan 4, 2018 at 10:36 AM Jernej Zidar <jernej.zidar at gmail.com 
> <mailto:jernej.zidar at gmail.com>> wrote:
>     Hi,
>     The "-deffnm" option is very handy because the user doesn't have
>     to specify every single output file (energy, trajectory, log,
>     checkpoint).
> But what's the requirement for renaming them? The default names are 
> fine - name collisions only arise when someone tries to do their 
> entire (sub)project in the same directory, which IMO is an anti-pattern.

To counter that, I train my students to ALWAYS use descriptive file 
names. Of course one can have a variety of organizational schemes, but 
training someone who is new to MD is difficult if they just have a lot 
of generically named files, because a lot of the initial concepts are 
somewhat abstract.

"What's in traj.trr?" (student gives blank stare)
"What's in md_20_30.trr?" (student says "the trajectory data from 20-30 ns")

The connection is obvious in how one assembles proper inputs and uses 
previous output to move forward.

I, for one, would HATE to lose -deffnm. It's going to make teaching new 
users more difficult and it's going to break every script I have.


>     This option should be kept if it is not too much trouble.
> The trouble is not the simple case, where it works fine. The trouble 
> is the forest of files that get written by all the modules. There's a 
> lot of infrastructure (and test cases) needed so that all combinations 
> of e.g. mdrun -deffnm -multi -px -append work reliably, now, and under 
> maintenance.
>     Personally, I'd like to see this option applied to other tools as
>     well (trjconv for example).
> What's an example use case, please?
>     One suggestion: Would it be possible to have all the tools that
>     analyze trajectories aware of the "-tu" switch ? It's way more
>     convenient to specify the time in ns, ms, ... than in number of
>     steps.
> Maybe, but perhaps you are referring to -b and -t (which take input in 
> ps, not steps). Again, there's a lot of infrastructure and testing 
> needed to make that work (and potentially confusing if any other 
> time-related option is not also similarly customizable). We've 
> historically done a poor job of that, and now have about as much debt 
> as assets... I don't see enough value in
> gmx tool -tu ns -b 10 -e 20
> vs
> gmx tool -b 10000 -e 20000
> for someone to want to put their time into it.
> Mark
>     Comments?
>     Cheers,
>     Jernej Zidar
>     On Thu, Jan 4, 2018 at 5:15 PM, Mark Abraham
>     <mark.j.abraham at gmail.com <mailto:mark.j.abraham at gmail.com>> wrote:
>         We should also be aware that -deffnm is brittle in the same
>         way that -multi is, because our filename-handling machinery
>         doesn't centralize changing the prefix/suffix needed to
>         support -deffnm or -multi. So I think we should plan to
>         announce -deffnm as deprecated in the 2019 release (and remove
>         after that). If we think that's useful enough to want to keep,
>         we need people to put up their hands for the work to make all
>         the mdrun modules work with it.
>         Thanks,
>         Mark
>     --
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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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