[gmx-users] Multiple output trajectories with different sampling frequencies

Machtens, Jan-Philipp j.machtens at fz-juelich.de
Wed Jul 8 15:00:56 CEST 2015

Dear all,
I have a problem where I am interested in fast processes in one part
of the system and a slow process in another, distinct part of the system. Due to disk space limitation,
I would like mdrun to write (either compressed or full precision) output trajectories for different parts of the system at different output/sampling frequencies.

GROMACS does not take into account distinct parameters for compressed-x-grps, right ?
I mean the second nstxout-compressed and compressed-x-precision parameters are not taken into account:
    ; Output frequency and precision for .xtc file
    nstxout-compressed       = 1 100
    compressed-x-precision   = 1000 1000
    compressed-x-grps        = Protein System_&_!Protein

As a workaround I could write the whole system at low sampling rate to an uncompressed trajectory, and
one part of the system could be written at high frequency to a compressed trajectory.
But what if I want a trr file also for the "high-frequency sampling group" ?

Do you know solutions better than writing the whole system to a full precision trajectory at high sampling frequency,
followed by post-processing and possibly deleting the initial raw trajectory?

Many thanks!

Dr. Jan-Philipp Machtens
Institute of Complex Systems - Zelluläre Biophysik (ICS-4)
Forschungszentrum Jülich, Germany

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Prof. Dr. Sebastian M. Schmidt

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