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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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