[gmx-developers] XML files

Erik Lindahl lindahl at stanford.edu
Thu Mar 21 18:31:51 CET 2002

David van der Spoel wrote:

>I have started working on the GROMACS XML files again. I can now generate
>a subset of the tpx file in XML from grompp. Before I implement it all I
>would like to ask youto have a look at the gromacs.dtd (Data Type
>Description) file in your local share/top directory, and let me know if
>things are utterly wrong...
>As I see it, in GROMACS 4.0 we will completely move to XML, meaning tpr
>files will be read only.
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'.

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 way it will still be easy to edit options and topologies without 
loading huge file into emacs.

I'll think of ways we can separate topologies from forcefields.

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!



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