[gmx-users] Cutting and Pasting Trajectory Files

[K.A.Feenstra]

Christoph Meier wrote:
> 
> Dear All,
> 
> I am trying to transfer GROMACS trajectory files (.trr and .xtc) from a remote
> computer to my machine via FTP. Because of the size of these files, I cannot
> transfer them in one go - I need to break them into smaller pieces and
> transfer these individually.
> 
> Is there a clever way of doing this ?
> 
> If I break the tranjectories up into smaller pieces which correspond to a
> parts of the trajectory, transfer them and then join them, will I get
> one file which is identical to my original & intact trajectory ?
> Do I not lose some information (e.g. at the borderline between pieces)
> by cutting the trajectory into pieces ?
> Does this work for both .xtc and .trr files ?

you can use the unix tool 'split' to separate you file into pieces,
and use 'cat' to combine them later on. This works for any file and
will re-create the exact original. But you will get half-frames on
the borders of your (temporary) intermediate split file.

If you want the temporary files split on frame boundaries (but this
is not necessary), you need to use trjconv with the -b and -e options,
once for each fragment. Then, use trjcat to re-assemble the pieces.
trjcat will take care of any possible duplicate frames, and will
complain if any frames appear missing. This will work for any
trajectory type.

-- 
Groetjes,

Anton
 _____________ _____________________________________________________
|             | Anton Feenstra       Dept. of Biophysical Chemistry |
|  _   _  ___,| K.A.Feenstra at chem.rug.nl    University of Groningen |
| / \ / \'| | | Tel +31 50 363 4327                    Nijenborgh 4 |
|(   |   )| | | Fax +31 50 363 4800               9747 AG Groningen |
| \_/ \_/ | | | http://md.chem.rug.nl/~anton        The Netherlands |
|             | "Make the Floor Burn" (2 Unlimited)                 |
|_____________|_____________________________________________________|