1GMX-TRAJECTORY(1) GROMACS GMX-TRAJECTORY(1)
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6 gmx-trajectory - Print coordinates, velocities, and/or forces for se‐
7 lections
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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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19 gmx trajectory plots coordinates, velocities, and/or forces for pro‐
20 vided selections. By default, the X, Y, and Z components for the re‐
21 quested 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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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: xmgrace, xmgr, none
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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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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 2022, GROMACS development team
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1202022.2 Jun 16, 2022 GMX-TRAJECTORY(1)