On 28/09/2011 9:11 AM, Martin Kamp Jensen wrote:
On Tue, Sep 27, 2011 at 3:09 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> 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
========================================
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
