Man page - gmx-distance(1)
Packages contains this manual
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apt-get install gromacs-data
Manual
GMX-DISTANCE
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
NAME
gmx-distance - Calculate distances between pairs of positions
SYNOPSIS
gmx distance
[
-f
[<.xtc/.trr/...>]
] [
-s
[<.tpr/.gro/...>]
] [
-n
[<.ndx>]
]
[
-oav
[<.xvg>]
] [
-oall
[<.xvg>]
] [
-oxyz
[<.xvg>]
]
[
-oh
[<.xvg>]
] [
-oallstat
[<.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>
] [
-len
<real>
]
[
-tol
<real>
] [
-binw
<real>
]
DESCRIPTION
gmx distance calculates distances between pairs of positions as a function of time. Each selection specifies an independent set of distances to calculate. Each selection should consist of pairs of positions, and the distances are computed between positions 1-2, 3-4, etc.
-oav writes the average distance as a function of time for each selection. -oall writes all the individual distances. -oxyz does the same, but the x, y, and z components of the distance are written instead of the norm. -oh writes a histogram of the distances for each selection. The location of the histogram is set with -len and -tol . Bin width is set with -binw . -oallstat writes out the average and standard deviation for each individual distance, calculated over the frames.
Note that gmx distance calculates distances between fixed pairs (1-2, 3-4, etc.) within a single selection. To calculate distances between two selections, including minimum, maximum, and pairwise distances, use gmx pairdist .
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:
-oav [<.xvg>] (distave.xvg) (Optional)
Average distances as function of time
-oall [<.xvg>] (dist.xvg) (Optional)
All distances as function of time
-oxyz [<.xvg>] (distxyz.xvg) (Optional)
Distance components as function of time
-oh [<.xvg>] (disthist.xvg) (Optional)
Histogram of the distances
-oallstat [<.xvg>] (diststat.xvg) (Optional)
Statistics for individual distances
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: xmgrace, xmgr, none
-[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>
Position pairs to calculate distances for
-len <real> (0.1)
Mean distance for histogramming
-tol <real> (1)
Width of full distribution as fraction of -len
-binw <real> (0.001)
Bin width for histogramming
SEE ALSO
gmx(1)
More information about GROMACS is available at <- http://www.gromacs.org/ >.
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2025, GROMACS development team