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]
gmx mindist 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.
-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.
-or, minimum distances to each residue in the first
group are determined and plotted as a function of residue number.
-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
-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 gmx distance and gmx pairdist calculate distances.
Options to specify input files:
-s[<.tpr/.gro/…>] (topol.tpr) (Optional)
-n[<.ndx>] (index.ndx) (Optional)
Options to specify output files:
-on[<.xvg>] (numcont.xvg) (Optional)
-o[<.out>] (atm-pair.out) (Optional)
Generic output file
-ox[<.xtc/.trr/…>] (mindist.xtc) (Optional)
-or[<.xvg>] (mindistres.xvg) (Optional)
Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
Unit for time values: fs, ps, ns, us, ms, s
xvg plot formatting: xmgrace, xmgr, none
Calculate half a matrix of group-group distances
Calculate maximum distance instead of minimum
Distance for contacts
Count contacts with multiple atoms in the first group as one
Calculate minimum distance with periodic images
Split graph where time is zero
Number of secondary groups to compute distance to a central group
Take periodic boundary conditions into account
When writing per-residue distances, write distance for each time point
Write residue names