# gmx-distance man page

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: 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>

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