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

[David van der Spoel]

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