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

[Mark Abraham]

Hi,

On Wed, Jul 8, 2015 at 3:01 PM Machtens, Jan-Philipp <
j.machtens at fz-juelich.de> wrote:

> 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 ?
>

Right, these take a single field (the first one).


> 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?
>

There is no support in GROMACS for simplifying that workflow.

In principle, the TNG support in GROMACS 5 makes available a file format
that can handle writing such customized output (different groups at
different precision and/or frequency) to a single file, but neither the
.mdp input format nor mdrun has been extended to support actually writing
such files.

Mark


> Many thanks!
>
> Cheers,
> ====================================
> Dr. Jan-Philipp Machtens
> Institute of Complex Systems - Zelluläre Biophysik (ICS-4)
> Forschungszentrum Jülich, Germany
> ====================================
>
>
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