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

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 cen-
       ter 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 con-
       strained	degrees	of freedom!  This implies -com.

       Options -ekt and	-ekr plot the translational and	rotational kinetic en-
       ergy  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  vec-
       tor  is	plotted. In addition in	the same graph the kinetic energy dis-
       tribution is given.

       See gmx trajectory for plotting similar data for	selections.

OPTIONS
       Options to specify input	files:

       -f [<.xtc/.trr/^a|>] (traj.xtc)
	      Trajectory: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/^a|>] (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/^a|>] (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)
	      Time of first frame to read from trajectory (default unit	ps)

       -e <time> (0)
	      Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
	      Only use frame when t MOD	dt = first time	(default unit 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> (xmgrace)
	      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 instead of 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 aver-
	      age x

       -scale <real> (0)
	      Scale factor for .pdb output, 0 is autoscale

SEE ALSO
       gmx(1)

       More	information    about	GROMACS	   is	 available    at    <-
       http://www.gromacs.org/>.

COPYRIGHT
       2021, GROMACS development team

2021.3				 Aug 18, 2021			   GMX-TRAJ(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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