Provided by: gromacs-data_2019.3-2_all #### 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: 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

```

#### SEEALSO

```       gmx(1)

```       2019, GROMACS development team