gmx-distance - Calculate distances between pairs of positions

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                   GMX-DISTANCE(1)

gmxdistance  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  gmxdistance  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 gmxpairdist.

       gmx-distance - Calculate distances between pairs of positions

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)(Optional)
              Input trajectory or single configuration: xtctrrcptgrog96pdbtng-s[<.tpr/.gro/...>](topol.tpr)(Optional)
              Input structure: tprgrog96pdb 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: xmgrace, xmgr, none

       -[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

gmx(1)

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

          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>]