Provided by: gromacs-data_2019.3-2_all bug

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

       2019, GROMACS development team