[gmx-users] Problem with trjcat
k.a.feenstra at chem.rug.nl
Mon Dec 17 15:16:19 CET 2001
Marc Baaden wrote:
> I am doing consecutive minimization yielding gro
> files and trr files. I would like to cat either one
> together to one trajectory showing all consecutive minimizations.
> With gmx2.0 trjcat it works (at least catting the gro files)
> With gmx3.0 I always get the error
> Last frame 0 time 46.000
> Fatal error:
> Couldn't read time from second frame.
> (I only write out the last frame of each minimization, so there is
> only 1 frame in the trr file. And the gro file is one frame too,
trjcat is not very well suited for this pupose, since it will sort the
files on time stamp and will eleminiate any duplicate frames based on
The solution is actually quite trivial: use 'cat'. That will produce
valid concatenated .trr and .gro files. trjconv, but also all other
analysis programs, will read concatenated .gro files as a trajectory.
Time stamps in energy minimization are actually simply step numbers,
so the resulting 'time' sequence in the trajectory might be very
inconvenient, this you can change easily using 'trjconv -t0 0 -timestep 1',
or whatever you prefer.
| | Anton Feenstra Dept. of Biophysical Chemistry |
| _ _ ___,| K.A.Feenstra at chem.rug.nl University of Groningen |
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