1GMX-TRAJ(1) GROMACS GMX-TRAJ(1)
2
6 gmx-traj - Plot x, v, f, box, temperature and rotational energy from
7 trajectories
8
10 gmx traj [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
11 [-ox [<.xvg>]] [-oxt [<.xtc/.trr/...>]] [-ov [<.xvg>]]
12 [-of [<.xvg>]] [-ob [<.xvg>]] [-ot [<.xvg>]] [-ekt [<.xvg>]]
13 [-ekr [<.xvg>]] [-vd [<.xvg>]] [-cv [<.pdb>]] [-cf [<.pdb>]]
14 [-av [<.xvg>]] [-af [<.xvg>]] [-b <time>] [-e <time>]
15 [-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>] [-[no]com]
16 [-[no]pbc] [-[no]mol] [-[no]nojump] [-[no]x] [-[no]y]
17 [-[no]z] [-ng <int>] [-[no]len] [-[no]fp] [-bin <real>]
18 [-ctime <real>] [-scale <real>]
19
21 gmx 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.
26 Option -ot plots the temperature of each group, provided velocities are
28 present in the trajectory file. No corrections are made for con‐
29 strained degrees of freedom! This implies -com.
30 Options -ekt and -ekr plot the translational and rotational kinetic
32 energy of each group, provided velocities are present in the trajectory
33 file. This implies -com.
34 Options -cv and -cf write the average velocities and average forces as
36 temperature factors to a .pdb file with the average coordinates or the
37 coordinates at -ctime. The temperature factors are scaled such that
38 the maximum is 10. The scaling can be changed with the option -scale.
39 To get the velocities or forces of one frame set both -b and -e to the
40 time of desired frame. When averaging over frames you might need to use
41 the -nojump option to obtain the correct average coordinates. If you
42 select either of these option the average force and velocity for each
43 atom are written to an .xvg file as well (specified with -av or -af).
44 Option -vd computes a velocity distribution, i.e. the norm of the vec‐
46 tor is plotted. In addition in the same graph the kinetic energy dis‐
47 tribution is given.
48 See gmx trajectory for plotting similar data for selections.
50
52 Options to specify input files:
53 -f [<.xtc/.trr/…>] (traj.xtc)
55 Trajectory: xtc trr cpt gro g96 pdb tng
56 -s [<.tpr/.gro/…>] (topol.tpr)
58 Structure+mass(db): tpr gro g96 pdb brk ent
59 -n [<.ndx>] (index.ndx) (Optional)
61 Index file
62 Options to specify output files:
64 -ox [<.xvg>] (coord.xvg) (Optional)
66 xvgr/xmgr file
67 -oxt [<.xtc/.trr/…>] (coord.xtc) (Optional)
69 Trajectory: xtc trr cpt gro g96 pdb tng
70 -ov [<.xvg>] (veloc.xvg) (Optional)
72 xvgr/xmgr file
73 -of [<.xvg>] (force.xvg) (Optional)
75 xvgr/xmgr file
76 -ob [<.xvg>] (box.xvg) (Optional)
78 xvgr/xmgr file
79 -ot [<.xvg>] (temp.xvg) (Optional)
81 xvgr/xmgr file
82 -ekt [<.xvg>] (ektrans.xvg) (Optional)
84 xvgr/xmgr file
85 -ekr [<.xvg>] (ekrot.xvg) (Optional)
87 xvgr/xmgr file
88 -vd [<.xvg>] (veldist.xvg) (Optional)
90 xvgr/xmgr file
91 -cv [<.pdb>] (veloc.pdb) (Optional)
93 Protein data bank file
94 -cf [<.pdb>] (force.pdb) (Optional)
96 Protein data bank file
97 -av [<.xvg>] (all_veloc.xvg) (Optional)
99 xvgr/xmgr file
100 -af [<.xvg>] (all_force.xvg) (Optional)
102 xvgr/xmgr file
103 Other options:
105 -b <time> (0)
107 Time of first frame to read from trajectory (default unit ps)
108 -e <time> (0)
110 Time of last frame to read from trajectory (default unit ps)
111 -dt <time> (0)
113 Only use frame when t MOD dt = first time (default unit ps)
114 -tu <enum> (ps)
116 Unit for time values: fs, ps, ns, us, ms, s
117 -[no]w (no)
119 View output .xvg, .xpm, .eps and .pdb files
120 -xvg <enum> (xmgrace)
122 xvg plot formatting: xmgrace, xmgr, none
123 -[no]com (no)
125 Plot data for the com of each group
126 -[no]pbc (yes)
128 Make molecules whole for COM
129 -[no]mol (no)
131 Index contains molecule numbers instead of atom numbers
132 -[no]nojump (no)
134 Remove jumps of atoms across the box
135 -[no]x (yes)
137 Plot X-component
138 -[no]y (yes)
140 Plot Y-component
141 -[no]z (yes)
143 Plot Z-component
144 -ng <int> (1)
146 Number of groups to consider
147 -[no]len (no)
149 Plot vector length
150 -[no]fp (no)
152 Full precision output
153 -bin <real> (1)
155 Binwidth for velocity histogram (nm/ps)
156 -ctime <real> (-1)
158 Use frame at this time for x in -cv and -cf instead of the aver‐
159 age x
160 -scale <real> (0)
162 Scale factor for .pdb output, 0 is autoscale
163
165 gmx(1)
166 More information about GROMACS is available at <‐
168 http://www.gromacs.org/>.
169
171 2019, GROMACS development team
1722018.7 May 29, 2019 GMX-TRAJ(1)