gmx-pairdist - Calculate pairwise distances between groups of positions

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                   GMX-PAIRDIST(1)

gmxpairdist  calculates pairwise distances between one reference selection (given with -ref) and one or
       more other selections (given with -sel).  It can calculate either the minimum distance (the default),  or
       the  maximum  distance  (with  -typemax).   Distances to each selection provided with -sel are computed
       independently.

       By default, the global minimum/maximum distance is computed.  To compute more  distances  (e.g.,  minimum
       distances  to  each  residue  in -ref), use -refgrouping and/or -selgrouping to specify how the positions
       within each selection should be grouped.

       Computed distances are written to the file specified with -o.  If there are N groups in -ref and M groups
       in the first selection in -sel, then the output contains N*M columns for the first selection. The columns
       contain distances like this: r1-s1, r2-s1, ..., r1-s2, r2-s2, ..., where rn is the n'th group in -ref and
       sn is the n'th group in the other selection.  The distances for the second selection  comes  as  separate
       columns  after  the  first  selection,  and  so  on.   If  some selections are dynamic, only the selected
       positions are used in the computation but the same number of columns is always written out.  If there are
       no positions contributing to some group pair, then the cutoff value is written (see below).

       -cutoff sets a cutoff for the computed distances.  If the  result  would  contain  a  distance  over  the
       cutoff, the cutoff value is written to the output file instead. By default, no cutoff is used, but if you
       are  not interested in values beyond a cutoff, or if you know that the minimum distance is smaller than a
       cutoff, you should set this option to allow the tool to use grid-based  searching  and  be  significantly
       faster.

       If you want to compute distances between fixed pairs, gmxdistance may be a more suitable tool.

       gmx-pairdist - Calculate pairwise distances between groups 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:

       -o[<.xvg>](dist.xvg)
              Distances as function of time

       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

       -cutoff<real>(0)
              Maximum distance to consider

       -type<enum>(min)
              Type of distances to calculate: min, max

       -refgrouping<enum>(all)
              Grouping of -ref positions to compute the min/max over: all, res, mol, none

       -selgrouping<enum>(all)
              Grouping of -sel positions to compute the min/max over: all, res, mol, none

       -ref<selection>
              Reference positions to calculate distances from

       -sel<selection>
              Positions to calculate distances for

gmx(1)

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

          gmx pairdist [-f[<.xtc/.trr/...>]] [-s[<.tpr/.gro/...>]] [-n[<.ndx>]]
                       [-o[<.xvg>]] [-b<time>] [-e<time>] [-dt<time>]
                       [-tu<enum>] [-fgroup<selection>] [-xvg<enum>]
                       [-[no]rmpbc] [-[no]pbc] [-sf<file>] [-selrpos<enum>]
                       [-seltype<enum>] [-cutoff<real>] [-type<enum>]
                       [-refgrouping<enum>] [-selgrouping<enum>]
                       [-ref<selection>] [-sel<selection>]