gmx-mindist - Calculate the minimum distance between two groups

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                    GMX-MINDIST(1)

gmxmindist  computes  the  distance  between  one  group and a number of other groups. Both the minimum
       distance (between any pair of atoms from the respective groups) and the number of contacts within a given
       distance are written to two separate output files.  With the -group  option  a  contact  of  an  atom  in
       another  group  with  multiple  atoms in the first group is counted as one contact instead of as multiple
       contacts.  With -or, minimum distances to each residue in the first group are determined and plotted as a
       function of residue number.

       With option -pi the minimum distance of a group to its periodic image is  plotted.  This  is  useful  for
       checking  if  a protein has seen its periodic image during a simulation. Only one shift in each direction
       is considered, giving a total of 26 shifts. Note that periodicity information is required from  the  file
       supplied  with  with  -s,  either  as  a  .tpr file or a .pdb file with CRYST1 fields.  It also plots the
       maximum distance within the group and the lengths of the three box vectors.

       Also gmxdistance and gmxpairdist calculate distances.

       gmx-mindist - Calculate the minimum distance between two groups

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)
              Trajectory: xtctrrcptgrog96pdbtng-s[<.tpr/.gro/...>](topol.tpr)(Optional)
              Structure+mass(db): tprgrog96pdb brk ent

       -n[<.ndx>](index.ndx)(Optional)
              Index file

       Options to specify output files:

       -od[<.xvg>](mindist.xvg)
              xvgr/xmgr file

       -on[<.xvg>](numcont.xvg)(Optional)
              xvgr/xmgr file

       -o[<.out>](atm-pair.out)(Optional)
              Generic output file

       -ox[<.xtc/.trr/...>](mindist.xtc)(Optional)
              Trajectory: xtctrrgrog96pdbtng-or[<.xvg>](mindistres.xvg)(Optional)
              xvgr/xmgr file

       Other options:

       -b<time>(0)
              Time of first frame to read from trajectory (default unit ps)

       -e<time>(0)
              Time of last frame to read from trajectory (default unit ps)

       -dt<time>(0)
              Only use frame when t MOD dt = first time (default unit ps)

       -tu<enum>(ps)
              Unit for time values: fs, ps, ns, us, ms, s

       -[no]w(no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg<enum>(xmgrace)
              xvg plot formatting: xmgrace, xmgr, none

       -[no]matrix(no)
              Calculate half a matrix of group-group distances

       -[no]max(no)
              Calculate maximum distance instead of minimum

       -d<real>(0.6)
              Distance for contacts

       -[no]group(no)
              Count contacts with multiple atoms in the first group as one

       -[no]pi(no)
              Calculate minimum distance with periodic images

       -[no]split(no)
              Split graph where time is zero

       -ng<int>(1)
              Number of secondary groups to compute distance to a central group

       -[no]pbc(yes)
              Take periodic boundary conditions into account

       -[no]respertime(no)
              When writing per-residue distances, write distance for each time point

       -[no]printresname(no)
              Write residue names

gmx(1)

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

          gmx mindist [-f[<.xtc/.trr/...>]] [-s[<.tpr/.gro/...>]] [-n[<.ndx>]]
                      [-od[<.xvg>]] [-on[<.xvg>]] [-o[<.out>]]
                      [-ox[<.xtc/.trr/...>]] [-or[<.xvg>]] [-b<time>]
                      [-e<time>] [-dt<time>] [-tu<enum>] [-[no]w]
                      [-xvg<enum>] [-[no]matrix] [-[no]max] [-d<real>]
                      [-[no]group] [-[no]pi] [-[no]split] [-ng<int>]
                      [-[no]pbc] [-[no]respertime] [-[no]printresname]