g_mindist(1)
NAME
g_mindist - calculates the minimum distance between two groups
SYNOPSIS
g_mindist -f traj.xtc -s topol.tpr -n index.ndx -od mindist.xvg -on numcont.xvg -o atm-pair.out -ox mindist.xtc -or mindistres.xvg -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -[no]matrix -[no]max -d real -[no]pi -[no]split -ng int
DESCRIPTION
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 -or , minimum distances
to each residue in the first group are determined and plotted as a
function of reisdue 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
FILES
- -f traj.xtc Input
- Generic trajectory: xtc trr trj gro g96 pdb
- -s topol.tpr Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
- -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.
- Generic trajectory: xtc trr trj gro g96 pdb
- -or mindistres.xvg Output, Opt.
- xvgr/xmgr file
OTHER OPTIONS
- -[no]h no
- Print help 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: ps , fs , ns , us , ms , s , m or h
- -[no]w no
- View output xvg, xpm, eps and pdb files
- -[no]xvgr yes
- Add specific codes (legends etc.) in the output xvg files for the
- xmgrace program
- -[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]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
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.