Main Table of Contents

Fri 5 Jul 2013


g_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.

Other programs that calculate distances are g_dist and g_bond.


-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt. Index file
-od mindist.xvg Output xvgr/xmgr file
-on numcont.xvg Output, Opt. xvgr/xmgr file
-o atm-pair.out Output, Opt. Generic output file
-ox mindist.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb
-or mindistres.xvg Output, Opt. xvgr/xmgr file

Other options

-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-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 when t MOD dt = first time (ps)
-tu enum ps Time unit: fs, ps, ns, us, ms or s
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]matrix bool no Calculate half a matrix of group-group distances
-[no]max bool no Calculate *maximum* distance instead of minimum
-d real 0.6 Distance for contacts
-[no]group bool no Count contacts with multiple atoms in the first group as one
-[no]pi bool no Calculate minimum distance with periodic images
-[no]split bool no Split graph where time is zero
-ng int 1 Number of secondary groups to compute distance to a central group
-[no]pbc bool yes Take periodic boundary conditions into account
-[no]respertime bool no When writing per-residue distances, write distance for each time point
-[no]printresname bool no Write residue names