GMX-DISTANCE(1) GROMACS GMX-DISTANCE(1)

# 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:

Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng
Input structure: tpr gro g96 pdb brk ent
Extra index groups

Options to specify output files:

Average distances as function of time
All distances as function of time
Distance components as function of time
Histogram of the distances
Statistics for individual distances

Other options:

First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame if t MOD dt == first time (ps)
Unit for time values: fs, ps, ns, us, ms, s
Atoms stored in the trajectory file (if not set, assume first N atoms)
Plot formatting: none, xmgrace, xmgr
-[no]rmpbc (yes)
Make molecules whole for each frame
-[no]pbc (yes)
Use periodic boundary conditions for distance calculation
Provide selections from files
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
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
Position pairs to calculate distances for
Mean distance for histogramming
Width of full distribution as fraction of -len
Bin width for histogramming