g_traj(1)

1g_traj(1)                 GROMACS suite, VERSION 4.5                 g_traj(1)
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3
4

NAME

6       g_traj  -  plots  x, v and f of selected atoms/groups (and more) from a
7       trajectory
8
9       VERSION 4.5
10

SYNOPSIS

12       g_traj -f  traj.xtc  -s  topol.tpr  -n  index.ndx  -ox  coord.xvg  -oxt
13       coord.xtc  -ov  veloc.xvg  -of  force.xvg -ob box.xvg -ot temp.xvg -ekt
14       ektrans.xvg -ekr ekrot.xvg -vd veldist.xvg -cv veloc.pdb -cf  force.pdb
15       -av  all_veloc.xvg  -af  all_force.xvg -[no]h -[no]version -nice int -b
16       time -e time -dt time -tu  enum  -[no]w  -xvg  enum  -[no]com  -[no]pbc
17       -[no]mol -[no]nojump -[no]x -[no]y -[no]z -ng int -[no]len -[no]fp -bin
18       real -scale real
19

DESCRIPTION

21       g_traj plots coordinates, velocities,  forces  and/or  the  box.   With
22       -com the coordinates, velocities and forces are calculated for the cen‐
23       ter of mass of each group.  When  -mol is set, the numbers in the index
24       file are interpreted as molecule numbers and the same procedure as with
25        -com is used for each molecule.
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27
28       Option  -ot plots the temperature of each  group,  provided  velocities
29       are  present  in the trajectory file.  No corrections are made for con‐
30       strained degrees of freedom!  This implies  -com.
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32
33       Options  -ekt and  -ekr plot the translational and  rotational  kinetic
34       energy of each group, provided velocities are present in the trajectory
35       file.  This implies  -com.
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38       Options  -cv and  -cf write the average velocities and  average  forces
39       as  temperature factors to a pdb file with the average coordinates. The
40       temperature factors are scaled such that the maximum is 10. The scaling
41       can be changed with the option  -scale. To get the velocities or forces
42       of one frame set both  -b and  -e to the time of  desired  frame.  When
43       averaging  over  frames  you  might  need to use the  -nojump option to
44       obtain the correct average coordinates.  If you select either of  these
45       option  the  average force and velocity for each atom are written to an
46       xvg file as well (specified with  -av or  -af).
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49       Option  -vd computes a velocity distribution, i.e. the norm of the vec‐
50       tor  is  plotted. In addition in the same graph the kinetic energy dis‐
51       tribution is given.
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FILES

54       -f traj.xtc Input
55        Trajectory: xtc trr trj gro g96 pdb cpt
56
57       -s topol.tpr Input
58        Structure+mass(db): tpr tpb tpa gro g96 pdb
59
60       -n index.ndx Input, Opt.
61        Index file
62
63       -ox coord.xvg Output, Opt.
64        xvgr/xmgr file
65
66       -oxt coord.xtc Output, Opt.
67        Trajectory: xtc trr trj gro g96 pdb cpt
68
69       -ov veloc.xvg Output, Opt.
70        xvgr/xmgr file
71
72       -of force.xvg Output, Opt.
73        xvgr/xmgr file
74
75       -ob box.xvg Output, Opt.
76        xvgr/xmgr file
77
78       -ot temp.xvg Output, Opt.
79        xvgr/xmgr file
80
81       -ekt ektrans.xvg Output, Opt.
82        xvgr/xmgr file
83
84       -ekr ekrot.xvg Output, Opt.
85        xvgr/xmgr file
86
87       -vd veldist.xvg Output, Opt.
88        xvgr/xmgr file
89
90       -cv veloc.pdb Output, Opt.
91        Protein data bank file
92
93       -cf force.pdb Output, Opt.
94        Protein data bank file
95
96       -av all_veloc.xvg Output, Opt.
97        xvgr/xmgr file
98
99       -af all_force.xvg Output, Opt.
100        xvgr/xmgr file
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102

OTHER OPTIONS

104       -[no]hno
105        Print help info and quit
106
107       -[no]versionno
108        Print version info and quit
109
110       -nice int 19
111        Set the nicelevel
112
113       -b time 0
114        First frame (ps) to read from trajectory
115
116       -e time 0
117        Last frame (ps) to read from trajectory
118
119       -dt time 0
120        Only use frame when t MOD dt = first time (ps)
121
122       -tu enum ps
123        Time unit:  fs,  ps,  ns,  us,  ms or  s
124
125       -[no]wno
126        View output xvg, xpm, eps and pdb files
127
128       -xvg enum xmgrace
129        xvg plot formatting:  xmgrace,  xmgr or  none
130
131       -[no]comno
132        Plot data for the com of each group
133
134       -[no]pbcyes
135        Make molecules whole for COM
136
137       -[no]molno
138        Index contains molecule numbers iso atom numbers
139
140       -[no]nojumpno
141        Remove jumps of atoms across the box
142
143       -[no]xyes
144        Plot X-component
145
146       -[no]yyes
147        Plot Y-component
148
149       -[no]zyes
150        Plot Z-component
151
152       -ng int 1
153        Number of groups to consider
154
155       -[no]lenno
156        Plot vector length
157
158       -[no]fpno
159        Full precision output
160
161       -bin real 1
162        Binwidth for velocity histogram (nm/ps)
163
164       -scale real 0
165        Scale factor for pdb output, 0 is autoscale
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NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO