[gmx-users] Using trjcat to subdivide a trajectory into two trajectories (depending on a criterion)
gmx3 at hotmail.com
Tue Mar 9 16:00:38 CET 2010
Catting trajectories without overlap can also simply be done with the cat command.
But you probably want to use trjconv -drop -dropunder (or -dropover)
> Date: Tue, 9 Mar 2010 14:49:18 +0100
> From: cseifert at bph.ruhr-uni-bochum.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Using trjcat to subdivide a trajectory into two trajectories (depending on a criterion)
> I have a protein, which jumps between two states during a long
> simulation. The two states are: open and close.
> I used g_mindist to find out in which state the protein is at any given
> time. My results are two lists of times.
> e.g. (timeframe: 20ps):
> open: 0ps 20ps 40ps 100ps 120ps
> close: 60ps 80ps 140ps 160ps
> Now, I want to subdivide my trajectory into two trajectories:
> Protein.xtc <- This is the long trajectory
> Protein_open.xtc <- This should be a trajectory of ONLY the open
> Protein_close.xtc <- This should be a trajectory of ONLY the close
> This is what I tried:
> > # Generate the Protein_open with the first frames:
> > trjcat -f Protein.xtc -o Protein_open.xtc -b 0 -e 40
> > # Elongate Protein_open:
> > trjcat -f Protein_open.xtc Protein.xtc -o Protein_open.xtc -b 100 -e
> This seems to work (at least a bit), but I lose some frames (lose means:
> the number of frames in Protein_open.xtc does not equal the number of
> times in my open state list). And gmxcheck tells me, that some timesteps
> do not match (e.g.: Reading frame 190 time 19240.000
> Timesteps at t=19260 don't match (20, 60)).
> It gets even worse, when I try to do the same with the close state,
> because then Protein_close.xtc does not start with time 0ps, but with
> time 60ps.
> Another problem appears, when I want to start with a trajectory, which
> consists only of a single timestep. The produced trajectory seems to be
> invalid. I guess, that a .xtc file consits of (at least) two structures.
> Does someone has any suggestions?
> I tried several combinations of -settime, -demux and -cat but could not
> solve this.
> M. Sc. Christian Seifert
> Molecular Biomechanics Group
> HITS gGmbH
> Schloß-Wolfsbrunnenweg 35
> 69118 Heidelberg
> phone: +49-6221-533254
> fax: +49 6221 533298
> email: christian.seifert at h-its.org
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