[gmx-developers] Shall we ditch gro and g96 files?

Allen Smith easmith at beatrice.rutgers.edu
Tue Apr 1 19:53:43 CEST 2008

In message <14cc10610804011004l59bf45f5q273c30a32733d4ec at mail.gmail.com> (on
1 April 2008 10:04:34 -0700), jchodera at gmail.com (John Chodera) wrote:
>To address a number of excellent comments and questions:
>On 01/04/2008, Erik Lindahl <lindahl at cbr.su.se> wrote:
>> I think a lot of people (including me...) like to be able to do "simple"
>> coordinate manipulation through scripts that just grep/awk for atom

Or otherwise manipulate them, yes, such as via Perl.

>> but I like Mathias suggestion of having a separate tool to translate
>> back/forth instead, and keep the "core" format HDF5.
>I agree that this is a much better idea than restricting the format to
>be ASCII.

Provided that there are ways to easily go back and forth, yes.

>Another drawback of ASCII that hasn't been mentioned is that it is
>impossible to represent the floating-point numbers in exactly the same
>way as they are used in gromacs.

Since they're base-10 not binary?

>If the existing formats are still supported, then it will be possible
>to work around these issues until they are resolved, at least in the
>majority of cases where the extra information that could be contained
>in netCDF and HDF5 is irrelevant.

This would be an argument for leaving in gro-format support, possibly as the
ASCII format to be available for script manipulation, and also as how
GROMACS could format its output if netCDF/HDF5 are not available.

>Regarding Berk's comments that he and David want a "flexible and
>extendible" format for manipulating single conformations before and
>after runs:

It'd also be nice if an ASCII format was available for manipulating
trajectory files, but that's less of a concern in most situations.

>I would remind you that there are convenient Python
>modules that make manipulation of this data very, very easy, even for
>quick scripts:

Helpful. How about Perl modules for HDF5? I note that a Perl interface comes
with NetCDF.


Allen Smith, Ph.D.                http://cesario.rutgers.edu/easmith/
February 1, 2003                               Space Shuttle Columbia
Ad Astra Per Aspera                     To The Stars Through Asperity

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