[gmx-users] Request for return of PDF containing all the commands, with help

Mark Abraham mark.j.abraham at gmail.com
Thu Sep 18 14:52:12 CEST 2014

On Thu, Sep 18, 2014 at 12:02 AM, Dallas Warren <Dallas.Warren at monash.edu>

> Can I put in a request to have the full list of GROMACS commands/scripts,
> along with their help text, added back to the end of the manual?  Or at
> least have a separate PDF available?

I doubt it will come back in its old form...

> What was the reason for removing that section?

... because the only way such documentation might stay up to date is to
generate it from the code. We'd like to make the documentation available in
a number of formats, because some people would like man gmx-grompp, others
gmx grompp -h, others a single webpage, and others some monolithic
all-tools format. The reference manual is written in LaTeX, so having the
compendium of tools documentation there in a non-hacky way means turning
whatever is in the code into LaTeX. Historically there were not good ways
to do that and produce the other formats, and so there was a parser written
in C embedded in each tool that would do grompp -man tex (or something, I
forget) and a lot of hoop-jumping C, shell and build-system code to make
our own custom markup language (since historically there was nothing good
we could use) that could be rendered into something sane in all those
formats. As part of the transition to using a single gmx tool, we
simplified life by removing support for writing LaTeX (and probably some
others too, I forget). Thus, Appendix D was doomed. See also extensive
discussion at http://redmine.gromacs.org/issues/685,
http://redmine.gromacs.org/issues/969 and
http://redmine.gromacs.org/issues/1242. Teemu has already done much heroic
work here ;-)

In the longer term, I would like to move away from LaTeX and towards
something for which we can use external parsing and presentation tools, and
which hopefully might integrate with our Doxygen code-documentation tool in
a way that lets us have user-level and developer-level documentation living
nearby, in the source code, and all being generated reasonably smoothly.

Over the years I have found having them all there on screen, in one place,
> easily browsable etc invaluable.

Depends how one browses, I guess :-) It is good to get feedback, thanks.

> See that there is a list on the website now
> http://manual.gromacs.org/programs/byname.html but having in PDF is
> better I think.

Change is always painful, but is it something about PDF that you're
missing, or is just having a monolithic webpage also a reasonable right-now


Catch ya,
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
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