[gmx-users] Combining energy files

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 27 15:09:41 CEST 2011

Martin Kamp Jensen wrote:
> Hello,
> 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?

Don't use the -cat option of trjcat.  Normally you'll have duplicate time 
frames, for instance, in the final frame of "first.xtc" and the first frame of 
"second.xtc."  If they are the same, you do not need to keep them.  The -cat 
option, as I understand it, is basically for fudging different trajectories 
together for non-standard purposes.  If you omit -cat then you'll have .edr and 
.xtc files that match.


> Regards,
> Martin.
> [1] http://manual.gromacs.org/online/trjcat.html
> [2] http://manual.gromacs.org/online/eneconv.html


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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