[gmx-users] Combining energy files
Mark.Abraham at anu.edu.au
Wed Sep 28 01:33:16 CEST 2011
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:
> 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  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 . 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
So pre-process with -settime such that duplicate times cannot arise.
> (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.)
>  http://manual.gromacs.org/online/trjcat.html
>  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
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