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

[John Chodera]

Gentlemen,

I know I don't chime in very often here, but I wanted to take this
opportunity to say that I very much support the idea of replacing the
limited-precision text-based formats like .gro, .pdb, and .g96 with
more flexible, portable, full-precision file formats.

Berk's suggestions of Espresso sounds very reasonable, but I would
encourage you to instead look at netCDF and HDF5:

netCDF:
http://www.unidata.ucar.edu/software/netcdf/

HDF5:
http://hdf.ncsa.uiuc.edu/HDF5/

Both of these formats provide easy-to-use libraries with APIs that
support nearly every language you could want to use (including C,
Fortran, and Python).  They provide platform-independent, extensible
formats for storing numerical information.  Both provide attribute
support, and HDF5 even allows hierarchical organization of objects,
making it very much like XML but with support for multidimensional
arrays of the same precision as used internally in gromacs.  The
libraries are robust, efficient, and well-supported.

AMBER, for example, has already moved to netCDF for their trajectory
format, though (unfortunately) not yet for their coordinate/restart
files.

http://amber.scripps.edu/netcdf/nctraj.html

Cheers,

John

--
Dr. John D. Chodera <jchodera at gmail.com>      | Mobile    : 415.867.7384
Postdoctoral researcher, Pande lab            | Lab phone : 650.723.1097
Department of Chemistry, Stanford University  | Lab fax   : 650.724.4021
http://www.dillgroup.ucsf.edu/~jchodera

On 29/03/2008, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Hi,
>
>  as you are aware all coordinate files have their drawbacks.
>  - gro & pdb have limited space for coordinates which is problematic for
>  simulating large systems
>  - pdb has no velocities
>  - gro & g96 can not store information on the element (i.e. can not
>  distinguish between Calpha and Calcium or Hgamma and Mercury, pdb can do
>  this)
>  - gro stores non-rectanular boxes in an awkward manner
>
>  I would therefore propose to make better coordinate file format that has
>  - coordinates
>  - velocities
>  - box as three edges and three angles (as in pdb file)
>  - atom name (and number)
>  - residue name and number
>  - element type (we could also introduce special elements for united
>  atoms or course grained particles, but they should not overlap with real
>  elements)
>  - variable format (no fixed column widths)
>
>  In order to encourage the use of such a more flexible file format I
>  would then propose that we remove the facility for writing gro and g96
>  files.
>
>  Please let me know what you think.
>
>  --
>  David van der Spoel, Ph.D.
>  Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>  Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
>  spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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