gmx trajectory¶
Synopsis¶
gmx trajectory [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-ox [<.xvg>]] [-ov [<.xvg>]] [-of [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>] [-tu <enum>] [-fgroup <selection>] [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>] [-seltype <enum>] [-select <selection>] [-[no]x] [-[no]y] [-[no]z] [-[no]len]
Description¶
gmx trajectory
plots coordinates, velocities, and/or forces for
provided selections. By default, the X, Y, and Z components for
the requested vectors are plotted, but specifying one or more of
-len
, -x
, -y
, and -z
overrides this.
For dynamic selections, currently the values are written out for all positions that the selection could select.
Options¶
Options to specify input files:
-f
[<.xtc/.trr/…>] (traj.xtc) (Optional)- Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng
-s
[<.tpr/.gro/…>] (topol.tpr) (Optional)- Input structure: tpr gro g96 pdb brk ent
-n
[<.ndx>] (index.ndx) (Optional)- Extra index groups
Options to specify output files:
-ox
[<.xvg>] (coord.xvg) (Optional)- Coordinates for each position as a function of time
-ov
[<.xvg>] (veloc.xvg) (Optional)- Velocities for each position as a function of time
-of
[<.xvg>] (force.xvg) (Optional)- Forces for each position as a function of time
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 if t MOD dt == first time (ps)
-tu
<enum> (ps)- Unit for time values: fs, ps, ns, us, ms, s
-fgroup
<selection>- Atoms stored in the trajectory file (if not set, assume first N atoms)
-xvg
<enum> (xmgrace)- Plot formatting: none, xmgrace, xmgr
-[no]rmpbc
(yes)- Make molecules whole for each frame
-[no]pbc
(yes)- Use periodic boundary conditions for distance calculation
-sf
<file>- Provide selections from files
-selrpos
<enum> (atom)- Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
-seltype
<enum> (atom)- Default selection output positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
-select
<selection>- Selections to analyze
-[no]x
(yes)- Plot X component
-[no]y
(yes)- Plot Y component
-[no]z
(yes)- Plot Z component
-[no]len
(no)- Plot vector length