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gmx-distance(1)                 GROMACS Manual                 gmx-distance(1)

NAME
       gmx-distance - Calculate distances between pairs of positions

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>]

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.

OPTIONS
       Options to specify input and output files:

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

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

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

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

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

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

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

       -oallstat [<.xvg>] (diststat.xvg) (Output, 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

       -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

       -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
       gromacs(7)

       More information about GROMACS is available at
       <http://www.gromacs.org/>.

VERSION 5.0.6                                                  gmx-distance(1)