1trjorder(1)               GROMACS suite, VERSION 4.5               trjorder(1)
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NAME

6       trjorder - orders molecules according to their distance to a group
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8       VERSION 4.5
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SYNOPSIS

11       trjorder  -f  traj.xtc -s topol.tpr -n index.ndx -o ordered.xtc -nshell
12       nshell.xvg -[no]h -[no]version -nice int -b time -e time -dt time  -xvg
13       enum -na int -da int -[no]com -r real -[no]z
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DESCRIPTION

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

43       -f traj.xtc Input
44        Trajectory: xtc trr trj gro g96 pdb cpt
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46       -s topol.tpr Input
47        Structure+mass(db): tpr tpb tpa gro g96 pdb
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49       -n index.ndx Input, Opt.
50        Index file
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52       -o ordered.xtc Output, Opt.
53        Trajectory: xtc trr trj gro g96 pdb
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55       -nshell nshell.xvg Output, Opt.
56        xvgr/xmgr file
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OTHER OPTIONS

60       -[no]hno
61        Print help info and quit
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63       -[no]versionno
64        Print version info and quit
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66       -nice int 19
67        Set the nicelevel
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69       -b time 0
70        First frame (ps) to read from trajectory
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72       -e time 0
73        Last frame (ps) to read from trajectory
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75       -dt time 0
76        Only use frame when t MOD dt = first time (ps)
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78       -xvg enum xmgrace
79        xvg plot formatting:  xmgrace,  xmgr or  none
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81       -na int 3
82        Number of atoms in a molecule
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84       -da int 1
85        Atom used for the distance calculation, 0 is COM
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87       -[no]comno
88        Use the distance to the center of mass of the reference group
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90       -r real 0
91        Cutoff used for the distance calculation when computing the number  of
92       molecules in a shell around e.g. a protein
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94       -[no]zno
95        Order molecules on z-coordinate
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SEE ALSO

99       gromacs(7)
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101       More   information  about  GROMACS  is  available  at  <http://www.gro‐
102       macs.org/>.
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106                                Thu 26 Aug 2010                    trjorder(1)