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

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2020, GROMACS development team