g_trjorder_d (1) - Linux Manuals
g_trjorder_d: orders molecules according to their distance to a group
NAMEtrjorder - orders molecules according to their distance to a group
SYNOPSIStrjorder -f traj.xtc -s topol.tpr -n index.ndx -o ordered.xtc -nshell nshell.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -na int -da int -[no]com -r real
DESCRIPTIONtrjorder orders molecules according to the smallest distance to atoms in a reference group. 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. All atoms in the trajectory are written to the output trajectory.
trjorder can be useful for e.g. analyzing the n waters closest to a protein. In that case the reference group would be the protein and the group of molecules would consist of all the water atoms. When an index group of the first n waters is made, the ordered trajectory can be used with any Gromacs program to analyze the n closest waters.
If the output file is a pdb file, the distance to the reference target will be stored in the B-factor field in order to color with e.g. rasmol.
With option -nshell the number of molecules within a shell of radius -r around the refernce group are printed.
FILES-f traj.xtc Input
-nice int 19
-b time 0
-e time 0
-dt time 0
-na int 3
-da int 1
-r real 0
More information about GROMACS is available at <http://www.gromacs.org/>.