1GMX-TRAJECTORY(1)                   GROMACS                  GMX-TRAJECTORY(1)
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NAME

6       gmx-trajectory  -  Print  coordinates,  velocities,  and/or  forces for
7       selections
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SYNOPSIS

10          gmx trajectory [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
11                       [-n [<.ndx>]] [-ox [<.xvg>]] [-ov [<.xvg>]]
12                       [-of [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
13                       [-tu <enum>] [-fgroup <selection>] [-xvg <enum>]
14                       [-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>]
15                       [-seltype <enum>] [-select <selection>] [-[no]x]
16                       [-[no]y] [-[no]z] [-[no]len]
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DESCRIPTION

19       gmx trajectory plots coordinates, velocities, and/or  forces  for  pro‐
20       vided  selections.  By  default,  the  X,  Y,  and Z components for the
21       requested vectors are plotted, but specifying one or more of -len,  -x,
22       -y, and -z overrides this.
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24       For  dynamic  selections,  currently the values are written out for all
25       positions that the selection could select.
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OPTIONS

28       Options to specify input files:
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30       -f [<.xtc/.trr/…>] (traj.xtc) (Optional)
31              Input trajectory or single configuration: xtc trr  cpt  gro  g96
32              pdb tng
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34       -s [<.tpr/.gro/…>] (topol.tpr) (Optional)
35              Input structure: tpr gro g96 pdb brk ent
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37       -n [<.ndx>] (index.ndx) (Optional)
38              Extra index groups
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40       Options to specify output files:
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42       -ox [<.xvg>] (coord.xvg) (Optional)
43              Coordinates for each position as a function of time
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45       -ov [<.xvg>] (veloc.xvg) (Optional)
46              Velocities for each position as a function of time
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48       -of [<.xvg>] (force.xvg) (Optional)
49              Forces for each position as a function of time
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51       Other options:
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53       -b <time> (0)
54              First frame (ps) to read from trajectory
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56       -e <time> (0)
57              Last frame (ps) to read from trajectory
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59       -dt <time> (0)
60              Only use frame if t MOD dt == first time (ps)
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62       -tu <enum> (ps)
63              Unit for time values: fs, ps, ns, us, ms, s
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65       -fgroup <selection>
66              Atoms  stored in the trajectory file (if not set, assume first N
67              atoms)
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69       -xvg <enum> (xmgrace)
70              Plot formatting: none, xmgrace, xmgr
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72       -[no]rmpbc (yes)
73              Make molecules whole for each frame
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75       -[no]pbc (yes)
76              Use periodic boundary conditions for distance calculation
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78       -sf <file>
79              Provide selections from files
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81       -selrpos <enum> (atom)
82              Selection reference positions: atom, res_com, res_cog,  mol_com,
83              mol_cog,     whole_res_com,     whole_res_cog,    whole_mol_com,
84              whole_mol_cog,   part_res_com,    part_res_cog,    part_mol_com,
85              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
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87       -seltype <enum> (atom)
88              Default  selection  output  positions:  atom,  res_com, res_cog,
89              mol_com, mol_cog, whole_res_com,  whole_res_cog,  whole_mol_com,
90              whole_mol_cog,    part_res_com,    part_res_cog,   part_mol_com,
91              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
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93       -select <selection>
94              Selections to analyze
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96       -[no]x (yes)
97              Plot X component
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99       -[no]y (yes)
100              Plot Y component
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102       -[no]z (yes)
103              Plot Z component
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105       -[no]len (no)
106              Plot vector length
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SEE ALSO

109       gmx(1)
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111       More    information    about    GROMACS    is    available    at     <‐
112       http://www.gromacs.org/>.
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115       2019, GROMACS development team
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1202019.4                           Oct 02, 2019                GMX-TRAJECTORY(1)
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