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. 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:
Options to specify output files:
Other options: