1 .TH trjorder 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
3 trjorder - orders molecules according to their distance to a group
5 .B VERSION 4.5.4-dev-20110404-bc5695c
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-o" " ordered.xtc "
12 .BI "\-nshell" " nshell.xvg "
14 .BI "\-[no]version" ""
26 \&\fB trjorder\fR orders molecules according to the smallest distance
27 \&to atoms in a reference group
28 \&or on z\-coordinate (with option \fB \-z\fR).
29 \&With distance ordering, it will ask for a group of reference
30 \&atoms and a group of molecules. For each frame of the trajectory
31 \&the selected molecules will be reordered according to the shortest
32 \&distance between atom number \fB \-da\fR in the molecule and all the
33 \&atoms in the reference group. The center of mass of the molecules can
34 \&be used instead of a reference atom by setting \fB \-da\fR to 0.
35 \&All atoms in the trajectory are written
36 \&to the output trajectory.
39 \&\fB trjorder\fR can be useful for e.g. analyzing the n waters closest to a
41 \&In that case the reference group would be the protein and the group
42 \&of molecules would consist of all the water atoms. When an index group
43 \&of the first n waters is made, the ordered trajectory can be used
44 \&with any Gromacs program to analyze the n closest waters.
48 \&If the output file is a \fB .pdb\fR file, the distance to the reference target
49 \&will be stored in the B\-factor field in order to color with e.g. Rasmol.
53 \&With option \fB \-nshell\fR the number of molecules within a shell
54 \&of radius \fB \-r\fR around the reference group are printed.
58 Trajectory: xtc trr trj gro g96 pdb cpt
60 .BI "\-s" " topol.tpr"
62 Structure+mass(db): tpr tpb tpa gro g96 pdb
64 .BI "\-n" " index.ndx"
68 .BI "\-o" " ordered.xtc"
70 Trajectory: xtc trr trj gro g96 pdb
72 .BI "\-nshell" " nshell.xvg"
78 Print help info and quit
80 .BI "\-[no]version" "no "
81 Print version info and quit
83 .BI "\-nice" " int" " 19"
86 .BI "\-b" " time" " 0 "
87 First frame (ps) to read from trajectory
89 .BI "\-e" " time" " 0 "
90 Last frame (ps) to read from trajectory
92 .BI "\-dt" " time" " 0 "
93 Only use frame when t MOD dt = first time (ps)
95 .BI "\-xvg" " enum" " xmgrace"
96 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
98 .BI "\-na" " int" " 3"
99 Number of atoms in a molecule
101 .BI "\-da" " int" " 1"
102 Atom used for the distance calculation, 0 is COM
104 .BI "\-[no]com" "no "
105 Use the distance to the center of mass of the reference group
107 .BI "\-r" " real" " 0 "
108 Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein
111 Order molecules on z\-coordinate
116 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.