debian man page for g_mindist

g_mindist(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_mindist(1)

NAME
       g_mindist - calculates the minimum distance between two groups

       VERSION 4.5.4-dev-20110404-bc5695c

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
       -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -[no]matrix -[no]max -d real -[no]group  -[no]pi  -[no]split  -ng
       int -[no]pbc -[no]respertime -[no]printresname

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  the   -group
       option  a  contact  of  an atom in other group with multiple atoms in the first group is counted as one contact instead of as multiple con-
       tacts.  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.

       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

       -[no]versionno
	Print version 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:  fs,  ps,  ns,  us,	ms or  s

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

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -[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]groupno
	Count contacts with multiple atoms in the first group as one

       -[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

       -[no]respertimeno
	When writing per-residue distances, write distance for each time point

       -[no]printresnameno
	Write residue names

SEE ALSO
       gromacs(7)

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

								  Mon 4 Apr 2011						      g_mindist(1)