[gmx-developers] suggestion: velocities.xtc

Jochen Hub jhub at gwdg.de
Tue Oct 17 13:34:41 CEST 2006

David van der Spoel wrote:
> Tsjerk Wassenaar wrote:
>> Hi,
>> Actually, I did modify GMX3.3.1 to write velocities to a .xtc file
>> and, although I do agree with the statements regarding the offsets and
>> the need for precision, I find that there is definite benefit of using
>> the .xtc format. The file is much smaller than a .trr file (using the
>> same precision as for the positions, three decimals), although twice
>> as large as the coordinate .xtc file.
>> Best,
>> Tsjerk
> I agree that it makes sense to do something like this. For most 
> analysis this will be sufficient and for restarts we have the trr. In 
> summary, we don't want to modify the existing format in order not to 
> break other programs (such ad VMD), so for version 4 we'll probably 
> make a new format.

The easiest way would probably be to leave the coordinates xtc format as 
it is (to avoid problems in, e.g., vmd) and optionally write out a 
second xtc file with the velocities. Even if the compression is worse 
than for the coordinates (and according to Tsjerk the compression is not 
that bad) it is still much better than having to deal with the trr which 
always has the coordinates in full precision.

However, for the long term development of gromacs this might not be an 
elegant solution, I admit...


Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de

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