[gmx-users] Combining energy files

Martin Kamp Jensen martin.kamp.jensen at gmail.com
Tue Sep 27 15:00:48 CEST 2011


I need to combine several trajectories (.xtc) and energy file (.edr) pairs.
In the end I need all the conformations of the trajectories and a specific
energy value for each of them.

To combine two trajectories, I use trjcat [1] like this:

trjcat -f first.xtc second.xtc -o combined.xtc -cat

Since I just need the conformations (the coordinates) and I do not care
about "step" and "time," I guess this is okay.

To combine two energy files, it seems like I should use eneconv [2].
Unfortunately, there is not an argument like "-cat" for trjcat, which means
that the tool will not include all energies from the input files in the
output file ("In case of double time frames the one in the later file is
used."). I should probably note that I do not need "Av. Energy" or "Sum
Energy," I just need the energy frames in the energy files concatenated so
that I can easily extract them and assign them to the correct conformations.

Any ideas?


[1] http://manual.gromacs.org/online/trjcat.html
[2] http://manual.gromacs.org/online/eneconv.html
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