gmx mindist
Main Table of Contents VERSION 5.0.5

Synopsis

gmx mindist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
            [-od [<.xvg>]] [-on [<.xvg>]] [-o [<.out>]]
            [-ox [<.xtc/.trr/...>]] [-or [<.xvg>]] [-nice ] [-b

Description

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 calculates distances.

Options

Options to specify input and output files:

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

-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, 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

http://www.gromacs.org