table of contents
trjorder(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | trjorder(1) |
NAME¶
trjorder - orders molecules according to their distance to a groupSYNOPSIS¶
trjorder -f traj.xtc -s topol.tpr -n index.ndx -o ordered.xtc -nshell nshell.xvg -[no]h -[no]version -nice int -b time -e time -dt time -xvg enum -na int -da int -[no]com -r real -[no]zDESCRIPTION¶
trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected molecules will be reordered according to the shortest distance between atom number -da in the molecule and all the atoms in the reference group. The center of mass of the molecules can be used instead of a reference atom by setting -da to 0. All atoms in the trajectory are written to the output trajectory.FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Structure+mass(db): tpr tpb tpa gro g96 pdb
Index 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)
xvg plot formatting: xmgrace, xmgr or none
Number of atoms in a molecule
Atom used for the distance calculation, 0 is COM
Use the distance to the center of mass of the reference group
Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein
Order molecules on z-coordinate
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |