[gmx-users] Redirecting trajectories from one gmx module to another

Mark Abraham mark.j.abraham at gmail.com
Mon Oct 13 11:41:39 CEST 2014


Unfortunately, Gromacs file handling wasn't designed with pipes in mind. In
particular, we often open a file, read its header to get some information,
and then go back and read the file again, which doesn't work well with
using pipes (see http://redmine.gromacs.org/issues/1489 for details).
Relaxing that would be very useful, but there's nobody currently working on

Work-arounds might include memory-mapping the temporary file, or doing the
analysis on pieces and combining the analysis results, but there's no magic


On Mon, Oct 13, 2014 at 10:32 AM, Machtens, Jan-Philipp <
j.machtens at fz-juelich.de> wrote:

> Hi,
> I would like to redirect gromacs trajectories from one gmx module to
> another, e.g. using a shell pipe...
> For example, analyzing a trajectory which is split into two files could be
> done
> using
> gmx trjcat -f traj.part1.xtc traj.part2.xtc -o traj.cat.xtc && gmx
> whatever -f traj.cat.xtc -o result
> I would like to save the time needed by the trjcat run and the additional
> disk space for the concatenated trajectory by using something like
> gmx trjcat -f traj.part1.xtc traj.part2.xtc | gmx whatever -f - -o result
> This doesn't work that easy. Does anyone know an existing solution ?
> Thanks!
> Jan-Philipp
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