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On 28/09/2011 9:11 AM, Martin Kamp Jensen wrote:
<blockquote
cite="mid:CAFVEjokXcbqaJyCEcp3JK5DdRjOGscH_wx=GSV3mdQk2CfJcyA@mail.gmail.com"
type="cite">
<div class="gmail_quote">On Tue, Sep 27, 2011 at 3:09 PM, Justin
A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span>
wrote:<br>
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<div><br>
<br>
Martin Kamp Jensen wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello,<br>
<br>
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.<br>
<br>
To combine two trajectories, I use trjcat [1] like this:<br>
<br>
trjcat -f first.xtc second.xtc -o combined.xtc -cat<br>
<br>
<br>
Since I just need the conformations (the coordinates) and
I do not care about "step" and "time," I guess this is
okay.<br>
<br>
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.<br>
<br>
Any ideas?<br>
<br>
</blockquote>
<br>
</div>
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.<br>
</blockquote>
<div><br>
</div>
<div>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.</div>
</div>
</blockquote>
<br>
So pre-process with -settime such that duplicate times cannot arise.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAFVEjokXcbqaJyCEcp3JK5DdRjOGscH_wx=GSV3mdQk2CfJcyA@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div><br>
</div>
<div>(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.)</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0
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<br>
-Justin
<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Regards,<br>
Martin.<br>
<br>
[1] <a moz-do-not-send="true"
href="http://manual.gromacs.org/online/trjcat.html"
target="_blank">http://manual.gromacs.org/online/trjcat.html</a><br>
[2] <a moz-do-not-send="true"
href="http://manual.gromacs.org/online/eneconv.html"
target="_blank">http://manual.gromacs.org/online/eneconv.html</a><br>
<br>
</blockquote>
<br>
</div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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