[gmx-developers] multiple xtc output files (optionally in chunks)

Carsten Kutzner ckutzne at gwdg.de
Fri Oct 19 14:16:00 CEST 2007


I wonder if we could have some new options for the XTC output of
trajectories (I would also volunteer to implement them).

The problem that we face in our group is the following. Since we do not
use a queueing system, the trajectories naturally get very large. This
is a headache for our backup system which has to backup each open file
as a whole, even if only a few bytes were added since the last backup.

What would be a nice solution is to allow two (or better multiple) XTC
output files with individual options (nstxtcout1, xtc-grps1,
nstxtcout2,..., similar to the new mdp pull options) and an extra
parameter nstxtcchop1 for when to close an XTC and start writing to a
new one.

You could then e.g. save your protein *without* water in one single,
small XTC file (nstxtcchop1=0) which is kept on disk for further
analysis, while the large trajectory with water is saved in several
chunks (and e.g. archived).

Please let me know what you think.


Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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