NAME

       gmx-pairdist - Calculate pairwise distances between groups of positions

SYNOPSIS

          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>]

DESCRIPTION

       gmx  pairdist  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  -type  max).   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, gmx distance may be a more suitable tool.

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:

       -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: 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

       -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

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2020, GROMACS development team