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

[David van der Spoel]

Erik Lindahl wrote:
> Hi,
> 
> On Mar 31, 2008, at 6:09 PM, David van der Spoel wrote:
>>>>
>>> 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.
> 
> Writing an extremely complex file format that can hold anything is 
> trivial - then we can simply go XML. The challenge, imho, is to have a 
> format that is simple enough that a vanilla fortran program can read it 
> without excessive efforts in string parsing.

In that case a g96 variant could be more useful.
BOX
10 10 10
END BOX
COORDINATES
1 2 3
2 3 4
END COORDINATES

> 
> 
>> What do you need to allow isotropic scaling of dodecahedrons and other 
>> triclinic boxes?
> 
> That's an internal problem, and should thus be handled internally in the 
> code, not by requiring a new box specification. To avoid rounding errors 
> the easiest option is to calculate the angles at the start of the run, 
> and make sure they don't change if we use isotropic scaling.
True enough, but why determine the angles from the vectors when we can 
store them explicitly?

> 
> Cheers,
> 
> Erik
> 
> ------------
> Erik Lindahl   <lindahl at cbr.su.se>  Backup: <erik.lindahl at gmail.com>
> Assistant Professor, Computational Structural Biology
> Center for Biomembrane Research, Dept. Biochemistry & Biophysics
> Stockholm University, SE-106 91 Stockholm, Sweden
> Tel: +46(0)8164675  Mobile: +46(0)704218767  Fax: mail a PDF instead
> 
> 
> 
> 
> _______________________________________________
> 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 thewww 
> 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++