This is the command gmx-traj that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
gmx-traj - Plot x, v, f, box, temperature and rotational energy from trajectories
SYNOPSIS
gmx traj [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
[-ox [<.xvg>]] [-oxt [<.xtc/.trr/...>]] [-ov [<.xvg>]]
[-of [<.xvg>]] [-ob [<.xvg>]] [-ot [<.xvg>]] [-ekt [<.xvg>]]
[-ekr [<.xvg>]] [-vd [<.xvg>]] [-cv [<.pdb>]] [-cf [<.pdb>]]
[-av [<.xvg>]] [-af [<.xvg>]] [-b <time>] [-e <time>]
[-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>] [-[no]com]
[-[no]pbc] [-[no]mol] [-[no]nojump] [-[no]x] [-[no]y]
[-[no]z] [-ng <int>] [-[no]len] [-[no]fp] [-bin <real>]
[-ctime <real>] [-scale <real>]
DESCRIPTION
gmx traj plots coordinates, velocities, forces and/or the box. With -com the coordinates,
velocities and forces are calculated for the center of mass of each group. When -mol is
set, the numbers in the index file are interpreted as molecule numbers and the same
procedure as with -com is used for each molecule.
Option -ot plots the temperature of each group, provided velocities are present in the
trajectory file. No corrections are made for constrained degrees of freedom! This
implies -com.
Options -ekt and -ekr plot the translational and rotational kinetic energy of each group,
provided velocities are present in the trajectory file. This implies -com.
Options -cv and -cf write the average velocities and average forces as temperature factors
to a .pdb file with the average coordinates or the coordinates at -ctime. The temperature
factors are scaled such that the maximum is 10. The scaling can be changed with the
option -scale. To get the velocities or forces of one frame set both -b and -e to the
time of desired frame. When averaging over frames you might need to use the -nojump option
to obtain the correct average coordinates. If you select either of these option the
average force and velocity for each atom are written to an .xvg file as well (specified
with -av or -af).
Option -vd computes a velocity distribution, i.e. the norm of the vector is plotted. In
addition in the same graph the kinetic energy distribution is given.
OPTIONS
Options to specify input files:
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/...>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Optional)
Index file
Options to specify output files:
-ox [<.xvg>] (coord.xvg) (Optional)
xvgr/xmgr file
-oxt [<.xtc/.trr/...>] (coord.xtc) (Optional)
Trajectory: xtc trr cpt gro g96 pdb tng
-ov [<.xvg>] (veloc.xvg) (Optional)
xvgr/xmgr file
-of [<.xvg>] (force.xvg) (Optional)
xvgr/xmgr file
-ob [<.xvg>] (box.xvg) (Optional)
xvgr/xmgr file
-ot [<.xvg>] (temp.xvg) (Optional)
xvgr/xmgr file
-ekt [<.xvg>] (ektrans.xvg) (Optional)
xvgr/xmgr file
-ekr [<.xvg>] (ekrot.xvg) (Optional)
xvgr/xmgr file
-vd [<.xvg>] (veldist.xvg) (Optional)
xvgr/xmgr file
-cv [<.pdb>] (veloc.pdb) (Optional)
Protein data bank file
-cf [<.pdb>] (force.pdb) (Optional)
Protein data bank file
-av [<.xvg>] (all_veloc.xvg) (Optional)
xvgr/xmgr file
-af [<.xvg>] (all_force.xvg) (Optional)
xvgr/xmgr file
Other options:
-b <time> (0)
First frame (ps) to read from trajectory
-e <time> (0)
Last frame (ps) to read from trajectory
-dt <time> (0)
Only use frame when t MOD dt = first time (ps)
-tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none
-[no]com (no)
Plot data for the com of each group
-[no]pbc (yes)
Make molecules whole for COM
-[no]mol (no)
Index contains molecule numbers iso atom numbers
-[no]nojump (no)
Remove jumps of atoms across the box
-[no]x (yes)
Plot X-component
-[no]y (yes)
Plot Y-component
-[no]z (yes)
Plot Z-component
-ng <int> (1)
Number of groups to consider
-[no]len (no)
Plot vector length
-[no]fp (no)
Full precision output
-bin <real> (1)
Binwidth for velocity histogram (nm/ps)
-ctime <real> (-1)
Use frame at this time for x in -cv and -cf instead of the average x
-scale <real> (0)
Scale factor for .pdb output, 0 is autoscale
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