g_mindist (1) - Linux Man Pages

g_mindist: calculates the minimum distance between two groups

NAME

g_mindist - calculates the minimum distance between two groups

VERSION 4.0.1

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 -[no]pbc

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
 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]hno
 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 or  s

-[no]wno
 View output xvg, xpm, eps and pdb files

-[no]xvgryes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-[no]matrixno
 Calculate half a matrix of group-group distances

-[no]maxno
 Calculate *maximum* distance instead of minimum

-d real 0.6
 Distance for contacts

-[no]pino
 Calculate minimum distance with periodic images

-[no]splitno
 Split graph where time is zero

-ng int 1
 Number of secondary groups to compute distance to a central group

-[no]pbcyes
 Take periodic boundary conditions into account

SEE ALSO

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.