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

[David van der Spoel]

Berk Hess wrote:
> 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:

OK that looks interesting. The question is then the interpretation of 
the strings, which are still somewhat cryptic in this example. For 
instance is "id"  an integer or a string? How is the program that reads 
this supposed to know? Are there pre-defined strings? E.g. pos seems to 
imply that there are three coordinates.
> 
> # 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.
What do you need to allow isotropic scaling of dodecahedrons and other 
triclinic boxes?

> 
>>
>> 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.
> 
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-developers-request at gromacs.org.


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++