[gmx-developers] XML files

[Anton Feenstra]

David van der Spoel wrote:
> 
> On Thu, 21 Mar 2002, Anton Feenstra wrote:
> 
> >Good. That should also mean that most things will then be up-and-down
> >wards compatible (that is, between any 4+ versions)?
>
> In principle yes, with proper versioning in the DTDs that should be
> possible. Further changes will be the demise of the following files:
> .top
> .itp
> .gro
> .mdp
> .tpr
> .tpb
> .tpa

Sounds good. Are you also already implementing the forcefield
independent topology, that was discussed before?

There is one issue, though, that I don't recall was mentioned
before. If you have a large system (around 10000 atoms), reading
in the .tpr file can be quite slow (even from the local disk on
the r12k octane I'm at), in the order of 10-20 seconds. This will
get worse since people are going towards even larger systems (isn't
that right Erik?). Do you have any idea what would be the 
performance impact of moving from .tpr to XML in that respect?

Another sideways related thing now comes to mind also. After
getting rid of the old non-portable binary topology .tpb, we still
have the old non-portable trajectory format (.trj). I don't know
of anyone still using it, but a problem is that you can not tell
on which type of machine it was written. So I would suggest to
either drop it, or add an identification of the machine type, so
we can issue a warning.

> Although conversion tools will be necessary of course.

gmx2xml? ;-)

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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