[gmx-developers] XML files

David van der Spoel spoel at xray.bmc.uu.se
Thu Mar 21 23:00:53 CET 2002

On Thu, 21 Mar 2002, Erik Lindahl wrote:

>Hi David,
>I'm just starting to grasp the XML formats, so I'll do some reading up 
>before I share any deeper thoughts about it.
>One thing, though: Since we rewriting things anyway, shouldn't we get 
>rid of all strange abbreviations in the input files? I.e., change things 
>like 'nstenergy' to e.g. 'energy_file_output_frequency'.
Yes and no. If you have to type it you want it to be short. The nested 
format of XML makes it somewhat clearer already:

<gromacs title="A mixture of water and methanol">

  <!-- inputrec holds variables for the dynamics runs -->
  <inputrec algorithm="bd" nsteps="100" delta-t="0.002">
    <output nstlog="10" nstenergy="1" nstxout="10" nstvout="10" />

So you "immediately see" (tm) that output is a subset of inputrec and 
inputrec a subset of gromacs. But looking at it: inputrec could be renamed 
to parameters, and many others could be clarified too.

>I still think it's a good idea to maintain three separate input files: 
>coordinates, topology and options.
>Actually, the best solution would be if all three of these could share 
>header definitions, etc, so you could either write
>mdrun -s file1.xml file2.xml file3.xml
>or concatenate them together and use it as
>mdrun -s file.xml

This will be possible, my preference would be something like
mdrun params.xml coords.xml topol.xml forcefield.xml

>This way it will still be easy to edit options and topologies without 
>loading huge file into emacs.
Actually there are special XML editors out there that read the DTD and let 
you select one of the options for e.g. eeltype, instead of having to 
remember all the possibilities.

>I'll think of ways we can separate topologies from forcefields.
The problem is merging topologies with force fields.

>We also need to keep the old trajectory formats as optional output too 
>until all programs like VMD, gOpenMol, etc, can read the XML formats. 
>And, we should implement support for the new formats in babel... So, 
>let's not remove any file types until we are sure everything else is 
>working in the new formats!
We'll keep trr and xtc obviously for space reasons, maybe we need to keep 
gro for a while...

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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