g_mindist(1)

NAME
g_mindist VERSION 3.2.0

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]matrix -[no]max -d real -[no]pi -[no]split

DESCRIPTION
g_mindist computes the distance between one group and a number of other groups. Both the minimum distance 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 -1
 First frame (ps) to read from trajectory -e time -1
 Last frame (ps) to read from trajectory -dt time -1
 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]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