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GMX-TRJORDER(1) GROMACS GMX-TRJORDER(1) NAME gmx-trjorder - Order molecules according to their distance to a group SYNOPSIS gmx trjorder [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-o [<.xtc/.trr/...>]] [-nshell [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>] [-xvg <enum>] [-na <int>] [-da <int>] [-[no]com] [-r <real>] [-[no]z] DESCRIPTION gmx trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected mole- cules will be reordered according to the shortest distance between atom number -da in the molecule and all the atoms in the reference group. The center of mass of the molecules can be used instead of a reference atom by setting -da to 0. All atoms in the trajectory are written to the output trajectory. gmx trjorder can be useful for e.g. analyzing the n waters closest to a protein. In that case the reference group would be the protein and the group of molecules would consist of all the water atoms. When an index group of the first n waters is made, the ordered trajectory can be used with any GROMACS program to analyze the n closest waters. If the output file is a .pdb file, the distance to the reference target will be stored in the B-factor field in order to color with e.g. Ras- mol. With option -nshell the number of molecules within a shell of radius -r around the reference group are printed. OPTIONS Options to specify input files: -f [<.xtc/.trr/...>] (traj.xtc) Trajectory: xtc trr cpt gro g96 pdb tng -s [<.tpr/.gro/...>] (topol.tpr) Structure+mass(db): tpr gro g96 pdb brk ent -n [<.ndx>] (index.ndx) (Optional) Index file Options to specify output files: -o [<.xtc/.trr/...>] (ordered.xtc) (Optional) Trajectory: xtc trr gro g96 pdb tng -nshell [<.xvg>] (nshell.xvg) (Optional) xvgr/xmgr file Other options: -b <time> (0) Time of first frame to read from trajectory (default unit ps) -e <time> (0) Time of last frame to read from trajectory (default unit ps) -dt <time> (0) Only use frame when t MOD dt = first time (default unit ps) -xvg <enum> (xmgrace) xvg plot formatting: xmgrace, xmgr, none -na <int> (3) Number of atoms in a molecule -da <int> (1) Atom used for the distance calculation, 0 is COM -[no]com (no) Use the distance to the center of mass of the reference group -r <real> (0) Cutoff used for the distance calculation when computing the num- ber of molecules in a shell around e.g. a protein -[no]z (no) Order molecules on z-coordinate SEE ALSO gmx(1) More information about GROMACS is available at <- http://www.gromacs.org/>. COPYRIGHT 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-TRJORDER(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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