gmx mindist#


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. 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 gmx distance and gmx pairdist calculate distances.


Options to specify input files:

-f [<.xtc/.trr/…>] (traj.xtc)

Trajectory: xtc trr cpt gro g96 pdb tng

-s [<.tpr/.gro/…>] (topol.tpr) (Optional)

Structure+mass(db): tpr gro g96 pdb 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: xtc trr gro g96 pdb tng

-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