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

[Berk Hess]

David van der Spoel 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)

I agree that we need a better format, but then we want a flexible format.
An example of a good format is the Espresso package format, which Gromacs
can read and write already. Here is an example file:

# comment ...
{variable {box_l 0.000000 0.000000 0.000000}}
{particles {id pos type q}
        {0 0.230000 0.628000 0.113000 0 0}
        {1 0.137000 0.626000 0.150000 0 0}
        {2 0.231000 0.589000 0.021000 0 0}
}

All fields and variables are optional and are not fixed order or format.

For the box I don't see why using angles would necessarily be an 
improvement.
If you want angles or box vectors depends on the application.

>
> 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.

I think this is neither necessary nor wanted.
Is can always be useful to be able to write format of other packages or 
old formats.
And I think that when we no longer have gro as the default format,
most people will no longer us it.

Berk.