Hi! 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 struktures Protein_close.xtc <- This should be a trajectory of ONLY the close struktures 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 120 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. Greets, Christian -- M. Sc. Christian Seifert Molecular Biomechanics Group HITS gGmbH Schloß-Wolfsbrunnenweg 35 69118 Heidelberg Germany phone: +49-6221-533254 fax: +49 6221 533298 email: [email protected] http://www.h-its.org http://www.eml-research.de _________________________________________________ Amtsgericht Mannheim / HRB 337446 Managing Directors: Dr. h.c. Klaus Tschira Prof. Dr.-Ing. Andreas Reuter -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
