[gmx-users] Combining energy files

[Mark Abraham]

On 28/09/2011 9:11 AM, Martin Kamp Jensen wrote:
> On Tue, Sep 27, 2011 at 3:09 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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.

So pre-process with -settime such that duplicate times cannot arise.

Mark

>
> (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
>         [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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
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