[gmx-users] Combining energy files

Martin Kamp Jensen martin.kamp.jensen at gmail.com
Wed Sep 28 01:11:17 CEST 2011

On Tue, Sep 27, 2011 at 3:09 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> 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.

But my purposes are non-standard and I need all of the conformations of both
(or more) input trajectories as well as the corresponding energy frames. I
see that, per the description of "-cat," time and step information will be
messed up, but that is not a problem.

(I have created a program that reads conformations from a trajectory and
assigns a specific energy value from a corresponding energy file to each of
the conformations. I just had a special case where I was asked to work with
several trajectories and energy files which were provided to me and it would
be nice to just concatenate them and then not introduce special
functionality in my program to handle it.)

> -Justin
>  Regards,
>> Martin.
>> [1] http://manual.gromacs.org/**online/trjcat.html<http://manual.gromacs.org/online/trjcat.html>
>> [2] http://manual.gromacs.org/**online/eneconv.html<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
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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