[gmx-users] Analyzing a trajectory split over multiple files

Nicolas nsapay at ucalgary.ca
Thu Nov 27 23:54:14 CET 2008

Suman Chakrabarty a écrit :
> On Wed, Nov 26, 2008 at 2:19 PM, Omer Markovitch <omermar at gmail.com> wrote:
>> On Tue, Nov 25, 2008 at 01:47, Suman Chakrabarty <suman at sscu.iisc.ernet.in>
>> wrote:
>>> Dear all,
>>> I have a very long trajectory split over a large number of files. What
>>> would be the most efficient way to use the analysis programs over them?
>>> Do they support multiple input for trajectory? Or I need to combine all
>>> files into a single one anyway?
>> You should analyze each individual part on its own, and output the raw data
>> of the result, then average the parts together.
>> For example - say you are interested in coordination number of molecule X:
>> For each part, output both the total number of X's found, plus the total
>> number of X neighbors found. The coordination number is then the sum of
>> neig. divided by the sum of X's, from ALL parts.
>> It might be an issue if each part has different time length, then averaging
>> the coordination number of each part might give more statistical weigh to
>> short parts then they should have.
>> In other words, you should first collect the data of each part together, and
>> only then avg..
>> --Omer.
> Thanks for your response Omer. But I am currently more interested in
> observing the time evolution of certain properties, e.g. radius of
> gyration etc. and their histogram over the full trajectory. So I must
> combine either trajectory files or the output analysis data.
> It would have been much easier if there was some way to concatenate
> the multiple .xvg files easily. Also, the analysis programs should be
> able to export the output data in raw 2 (or more) column format
> without all the formatting statements as an option.
Actually, there is:

grep -v "^#" *.xvg > concatenate.xvg

The -v "^#" will skip all the comment lines of your xvg files. Of 
course, this assumes that your xvg files are correctly named, i.e. 
file01.xvg, file02.xvg, etc. With a short shell script, you can easily 
re-add the comments at the beginning of your concatenate file, renumber 
the frames correctly, etc. It is more convenient to write a Python or a 
Perl script to do this kind of stuff, though.


> Regards,
> Suman.
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