.TH gmx-distance 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-distance \- Calculate distances between pairs of positions

.SH SYNOPSIS
gmx distance [\-f [<.xtc/.trr/...>]] [\-s [<.tpr/.tpb/...>]]
             [\-n [<.ndx>]] [\-oav [<.xvg>]] [\-oall [<.xvg>]]
             [\-oxyz [<.xvg>]] [\-oh [<.xvg>]] [\-oallstat [<.xvg>]]
             [\-b <time>] [\-e <time>] [\-dt <time>] [\-tu <enum>]
             [\-xvg <enum>] [\-[no]rmpbc] [\-[no]pbc] [\-sf <file>]
             [\-selrpos <enum>] [\-select <selection>] [\-len <real>]
             [\-tol <real>] [\-binw <real>]

.SH DESCRIPTION
\fBgmx distance\fR 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.

\fB\-oav\fR writes the average distance as a function of time for each selection. \fB\-oall\fR writes all the individual distances. \fB\-oxyz\fR does the same, but the x, y, and z components of the distance are written instead of the norm. \fB\-oh\fR writes a histogram of the distances for each selection. The location of the histogram is set with \fB\-len\fR and \fB\-tol\fR. Bin width is set with \fB\-binw\fR. \fB\-oallstat\fR writes out the average and standard deviation for each individual distance, calculated over the frames.

.SH OPTIONS
Options to specify input and output files:

.BI "\-f" " [<.xtc/.trr/...>] (traj.xtc) (Input, Optional)"
    Input trajectory or single configuration: xtc trr cpt trj gro g96 pdb tng

.BI "\-s" " [<.tpr/.tpb/...>] (topol.tpr) (Input, Optional)"
    Input structure: tpr tpb tpa gro g96 pdb brk ent

.BI "\-n" " [<.ndx>] (index.ndx) (Input, Optional)"
    Extra index groups

.BI "\-oav" " [<.xvg>] (distave.xvg) (Output, Optional)"
    Average distances as function of time

.BI "\-oall" " [<.xvg>] (dist.xvg) (Output, Optional)"
    All distances as function of time

.BI "\-oxyz" " [<.xvg>] (distxyz.xvg) (Output, Optional)"
    Distance components as function of time

.BI "\-oh" " [<.xvg>] (disthist.xvg) (Output, Optional)"
    Histogram of the distances

.BI "\-oallstat" " [<.xvg>] (diststat.xvg) (Output, Optional)"
    Statistics for individual distances


Other options:

.BI "\-b" " <time> (0)"
    First frame (ps) to read from trajectory

.BI "\-e" " <time> (0)"
    Last frame (ps) to read from trajectory

.BI "\-dt" " <time> (0)"
    Only use frame if t MOD dt == first time (ps)

.BI "\-tu" " <enum> (ps)"
    Unit for time values: fs, ps, ns, us, ms, s

.BI "\-xvg" " <enum> (xmgrace)"
    Plot formatting: none, xmgrace, xmgr

.BI "\-[no]rmpbc" "  (yes)"
    Make molecules whole for each frame

.BI "\-[no]pbc" "  (yes)"
    Use periodic boundary conditions for distance calculation

.BI "\-sf" " <file>"
    Provide selections from files

.BI "\-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

.BI "\-select" " <selection>"
    Position pairs to calculate distances for

.BI "\-len" " <real> (0.1)"
    Mean distance for histogramming

.BI "\-tol" " <real> (1)"
    Width of full distribution as fraction of \fB\-len\fR

.BI "\-binw" " <real> (0.001)"
    Bin width for histogramming


.SH SEE ALSO
.BR gromacs(7)

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