gmx-traj(1)

1GMX-TRAJ(1)                         GROMACS                        GMX-TRAJ(1)
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NAME

6       gmx-traj  -  Plot  x, v, f, box, temperature and rotational energy from
7       trajectories
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SYNOPSIS

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>]
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DESCRIPTION

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.
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27       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.
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31       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.
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35       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).
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45       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.
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49       See gmx trajectory for plotting similar data for selections.
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OPTIONS

52       Options to specify input files:
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54       -f [<.xtc/.trr/…>] (traj.xtc)
55              Trajectory: xtc trr cpt gro g96 pdb tng
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57       -s [<.tpr/.gro/…>] (topol.tpr)
58              Structure+mass(db): tpr gro g96 pdb brk ent
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60       -n [<.ndx>] (index.ndx) (Optional)
61              Index file
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63       Options to specify output files:
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65       -ox [<.xvg>] (coord.xvg) (Optional)
66              xvgr/xmgr file
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68       -oxt [<.xtc/.trr/…>] (coord.xtc) (Optional)
69              Trajectory: xtc trr cpt gro g96 pdb tng
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71       -ov [<.xvg>] (veloc.xvg) (Optional)
72              xvgr/xmgr file
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74       -of [<.xvg>] (force.xvg) (Optional)
75              xvgr/xmgr file
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77       -ob [<.xvg>] (box.xvg) (Optional)
78              xvgr/xmgr file
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80       -ot [<.xvg>] (temp.xvg) (Optional)
81              xvgr/xmgr file
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83       -ekt [<.xvg>] (ektrans.xvg) (Optional)
84              xvgr/xmgr file
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86       -ekr [<.xvg>] (ekrot.xvg) (Optional)
87              xvgr/xmgr file
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89       -vd [<.xvg>] (veldist.xvg) (Optional)
90              xvgr/xmgr file
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92       -cv [<.pdb>] (veloc.pdb) (Optional)
93              Protein data bank file
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95       -cf [<.pdb>] (force.pdb) (Optional)
96              Protein data bank file
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98       -av [<.xvg>] (all_veloc.xvg) (Optional)
99              xvgr/xmgr file
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101       -af [<.xvg>] (all_force.xvg) (Optional)
102              xvgr/xmgr file
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104       Other options:
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106       -b <time> (0)
107              Time of first frame to read from trajectory (default unit ps)
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109       -e <time> (0)
110              Time of last frame to read from trajectory (default unit ps)
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112       -dt <time> (0)
113              Only use frame when t MOD dt = first time (default unit ps)
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115       -tu <enum> (ps)
116              Unit for time values: fs, ps, ns, us, ms, s
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118       -[no]w (no)
119              View output .xvg, .xpm, .eps and .pdb files
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121       -xvg <enum> (xmgrace)
122              xvg plot formatting: xmgrace, xmgr, none
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124       -[no]com (no)
125              Plot data for the com of each group
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127       -[no]pbc (yes)
128              Make molecules whole for COM
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130       -[no]mol (no)
131              Index contains molecule numbers instead of atom numbers
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133       -[no]nojump (no)
134              Remove jumps of atoms across the box
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136       -[no]x (yes)
137              Plot X-component
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139       -[no]y (yes)
140              Plot Y-component
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142       -[no]z (yes)
143              Plot Z-component
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145       -ng <int> (1)
146              Number of groups to consider
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148       -[no]len (no)
149              Plot vector length
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151       -[no]fp (no)
152              Full precision output
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154       -bin <real> (1)
155              Binwidth for velocity histogram (nm/ps)
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157       -ctime <real> (-1)
158              Use frame at this time for x in -cv and -cf instead of the aver‐
159              age x
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161       -scale <real> (0)
162              Scale factor for .pdb output, 0 is autoscale
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COPYRIGHT

171       2019, GROMACS development team
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1762019.2                           Apr 16, 2019                      GMX-TRAJ(1)

NAME

SYNOPSIS

DESCRIPTION

OPTIONS

SEE ALSO

COPYRIGHT