g_mindist

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