1GMX-TRJORDER(1)                     GROMACS                    GMX-TRJORDER(1)
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NAME

6       gmx-trjorder - Order molecules according to their distance to a group
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SYNOPSIS

9          gmx trjorder [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                       [-o [<.xtc/.trr/...>]] [-nshell [<.xvg>]] [-b <time>]
11                       [-e <time>] [-dt <time>] [-xvg <enum>] [-na <int>]
12                       [-da <int>] [-[no]com] [-r <real>] [-[no]z]
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DESCRIPTION

15       gmx  trjorder  orders  molecules  according to the smallest distance to
16       atoms in a reference group or on z-coordinate (with option  -z).   With
17       distance  ordering,  it  will  ask for a group of reference atoms and a
18       group of molecules. For each frame of the trajectory the selected mole‐
19       cules will be reordered according to the shortest distance between atom
20       number -da in the molecule and all the atoms in  the  reference  group.
21       The  center of mass of the molecules can be used instead of a reference
22       atom by setting -da to 0.  All atoms in the trajectory are  written  to
23       the output trajectory.
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25       gmx trjorder can be useful for e.g. analyzing the n waters closest to a
26       protein.  In that case the reference group would be the protein and the
27       group  of molecules would consist of all the water atoms. When an index
28       group of the first n waters is made, the ordered trajectory can be used
29       with any GROMACS program to analyze the n closest waters.
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31       If the output file is a .pdb file, the distance to the reference target
32       will be stored in the B-factor field in order to color with  e.g.  Ras‐
33       mol.
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35       With option -nshell the number of molecules within a shell of radius -r
36       around the reference group are printed.
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OPTIONS

39       Options to specify input files:
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41       -f [<.xtc/.trr/…>] (traj.xtc)
42              Trajectory: xtc trr cpt gro g96 pdb tng
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44       -s [<.tpr/.gro/…>] (topol.tpr)
45              Structure+mass(db): tpr gro g96 pdb brk ent
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47       -n [<.ndx>] (index.ndx) (Optional)
48              Index file
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50       Options to specify output files:
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52       -o [<.xtc/.trr/…>] (ordered.xtc) (Optional)
53              Trajectory: xtc trr gro g96 pdb tng
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55       -nshell [<.xvg>] (nshell.xvg) (Optional)
56              xvgr/xmgr file
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58       Other options:
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60       -b <time> (0)
61              Time of first frame to read from trajectory (default unit ps)
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63       -e <time> (0)
64              Time of last frame to read from trajectory (default unit ps)
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66       -dt <time> (0)
67              Only use frame when t MOD dt = first time (default unit ps)
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69       -xvg <enum> (xmgrace)
70              xvg plot formatting: xmgrace, xmgr, none
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72       -na <int> (3)
73              Number of atoms in a molecule
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75       -da <int> (1)
76              Atom used for the distance calculation, 0 is COM
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78       -[no]com (no)
79              Use the distance to the center of mass of the reference group
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81       -r <real> (0)
82              Cutoff used for the distance calculation when computing the num‐
83              ber of molecules in a shell around e.g. a protein
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85       -[no]z (no)
86              Order molecules on z-coordinate
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SEE ALSO

89       gmx(1)
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91       More     information    about    GROMACS    is    available    at    <‐
92       http://www.gromacs.org/>.
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95       2019, GROMACS development team
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1002019.2                           Apr 16, 2019                  GMX-TRJORDER(1)
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