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Hi,<br><br>Catting trajectories without overlap can also simply be done with the cat command.<br><br>But you probably want to use trjconv -drop -dropunder (or -dropover)<br><br>Berk<br><br>> Date: Tue, 9 Mar 2010 14:49:18 +0100<br>> From: cseifert@bph.ruhr-uni-bochum.de<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Using trjcat to subdivide a trajectory into two trajectories (depending on a criterion)<br>> <br>> Hi!<br>> <br>> I have a protein, which jumps between two states during a long<br>> simulation. The two states are: open and close.<br>> <br>> I used g_mindist to find out in which state the protein is at any given<br>> time. My results are two lists of times.<br>> e.g. (timeframe: 20ps):<br>> open: 0ps 20ps 40ps 100ps 120ps<br>> close: 60ps 80ps 140ps 160ps<br>> <br>> Now, I want to subdivide my trajectory into two trajectories:<br>> Protein.xtc <- This is the long trajectory<br>> Protein_open.xtc <- This should be a trajectory of ONLY the open<br>> struktures<br>> Protein_close.xtc <- This should be a trajectory of ONLY the close<br>> struktures<br>> <br>> This is what I tried:<br>> > # Generate the Protein_open with the first frames:<br>> > trjcat -f Protein.xtc -o Protein_open.xtc -b 0 -e 40<br>> > # Elongate Protein_open:<br>> > trjcat -f Protein_open.xtc Protein.xtc -o Protein_open.xtc -b 100 -e<br>> 120<br>> <br>> This seems to work (at least a bit), but I lose some frames (lose means:<br>> the number of frames in Protein_open.xtc does not equal the number of<br>> times in my open state list). And gmxcheck tells me, that some timesteps<br>> do not match (e.g.: Reading frame 190 time 19240.000 <br>> Timesteps at t=19260 don't match (20, 60)).<br>> <br>> It gets even worse, when I try to do the same with the close state,<br>> because then Protein_close.xtc does not start with time 0ps, but with<br>> time 60ps.<br>> <br>> Another problem appears, when I want to start with a trajectory, which<br>> consists only of a single timestep. The produced trajectory seems to be<br>> invalid. I guess, that a .xtc file consits of (at least) two structures.<br>> <br>> Does someone has any suggestions?<br>> I tried several combinations of -settime, -demux and -cat but could not<br>> solve this.<br>> <br>> Greets,<br>> Christian<br>> <br>> -- <br>> M. Sc. Christian Seifert<br>> Molecular Biomechanics Group<br>> HITS gGmbH<br>> Schloß-Wolfsbrunnenweg 35<br>> 69118 Heidelberg<br>> Germany<br>> <br>> phone: +49-6221-533254<br>> fax: +49 6221 533298<br>> email: christian.seifert@h-its.org<br>> http://www.h-its.org <br>> http://www.eml-research.de<br>> _________________________________________________<br>> <br>> Amtsgericht Mannheim / HRB 337446<br>> Managing Directors: <br>> Dr. h.c. Klaus Tschira<br>> Prof. Dr.-Ing. Andreas Reuter<br>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
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