table of contents
g_mindist(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_mindist(1) |
NAME¶
g_mindist - calculates the minimum distance between two groupsSYNOPSIS¶
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]printresnameDESCRIPTION¶
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 contacts. With -or, minimum distances to each residue in the first group are determined and plotted as a function of residue number.FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Structure+mass(db): tpr tpb tpa gro g96 pdb
Index file
xvgr/xmgr file
xvgr/xmgr file
Generic output file
Trajectory: xtc trr trj gro g96 pdb
xvgr/xmgr file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
Time unit: fs, ps, ns, us, ms or s
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Calculate half a matrix of group-group distances
Calculate *maximum* distance instead of minimum
Distance for contacts
Count contacts with multiple atoms in the first group as one
Calculate minimum distance with periodic images
Split graph where time is zero
Number of secondary groups to compute distance to a central group
Take periodic boundary conditions into account
When writing per-residue distances, write distance for each time point
Write residue names
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |