[gmx-users] gmx angle memory consumption

Matthias Ernst matthias.ernst at physik.uni-freiburg.de
Tue Nov 21 13:30:38 CET 2017


I want to calculate dihedral angles for long trajectories at high
sampling rates using gmx angle as follows:

gmx angle -f traj.xtc -n dih_indices.ndx -ov dih.xvg -type dihedral -all

After some time, it completely fills my RAM without having written
anything to the output file.  As the system starts swapping, everything
becomes incredibly slow.
I thought gmx tools usually process trajectories frame-wise and output
immediately (or in some chunks), but this seems not to be the case here.
Could it be gmx angle is storing the values in RAM and only writes them
out at the end of the analysis?

Thanks a lot,


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