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

Dallas Warren Dallas.Warren at monash.edu
Fri Sep 19 02:19:02 CEST 2014

Thank you Mark for the detailed response.

Knew there had to be a good reason for it :)

> ... 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

Easier things are to do, more likely to stay up to date, and more time you guys can spend on important code improvements and features ;)

> 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 ;-)

Some long discussions there, had a skim through and thing have the generate gist of things.  And great to see the amount of thought and discussion that goes into the big issues.
> 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.

If the source is in one place, then means only have to maintain that one spot.

> 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 solution?

Yes, definitely.  You adapt to how things are, no matter how flawed, then when it is changed it is very awkward and easy to complain about it.

It is probably more to do with things being in one document, rather than being a PDF as such.  Though PDF are attractive as available offline and as a single file.  When using a script for the first time (or after some time since last used it) would have the old appendix open to the side of the window and use that as a prompter.  Though that is easily doable, of course, by simply using another terminal window to the side with the script help page displaying in it.  And the attractive thing previously too was had a single, offline document in which all was explained/presented about GROMACS.

A monolithic page with all on it would be great, as long as implementing it doesn't waste / consume someone's time to do so.

When I started using GROMACS every month or so I would read through the appendix with the list of the help for all the commands, discovering features and things that I could do / use that had missed previously.

And a big thumbs up to those over the years that have put together the manual.  It is a great document.  Anyone starting out with MD I tell them to read the first couple of chapters as it gives a very good, brief overview of MD in general.

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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