[gmx-developers] XML files

[Erik Lindahl]

David van der Spoel wrote:

>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.
>

Actually, it would be nice to have units on all output and step stuff, 
so you could say that you want
100 ps of simulation with 2 fs timestep, and energy file output every 10 
ps. I don't think it affects the DTD, though, so we can do that later.

Is it possible to include help texts with a longer description of each item?

>
>This will be possible, my preference would be something like
>mdrun params.xml coords.xml topol.xml forcefield.xml
>
Ok. We don't really have to put any restrictions on the names - mdrun 
can just read 'everything' and complain if something is missing or 
present in more than one file. I guess we should use the last occurence 
then...

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

Agreed; but it would be darn nice to have! By the way, since you've been 
doing NMR stuff - I think it would be nice to be able to use atom names 
instead of numbers when describing bonds, etc. What's the most common 
way people would be adding NMR or X-ray restraints, and how do they 
select their atoms?

>>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...
>
And some kind of file format that doesn't use RPC libraries..  Even if I 
rip the RPC stuff from linux we can't be sure it will work 'everywhere'. 
I don't have the slightest idea what will happen with 64-bit windows, 
for instance...

Cheers,

Erik