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.
-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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