g_sorient_d (1) - Linux Manuals
g_sorient_d: analyzes solvent orientation around solutes
NAMEg_sorient - analyzes solvent orientation around solutes
SYNOPSISg_sorient -f traj.xtc -s topol.tpr -n index.ndx -o sori.xvg -no snor.xvg -ro sord.xvg -co scum.xvg -rc scount.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]com -[no]v23 -rmin real -rmax real -cbin real -rbin real -[no]pbc
DESCRIPTIONg_sorient analyzes solvent orientation around solutes. It calculates two angles between the vector from one or more reference positions to the first atom of each solvent molecule: theta1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3.
theta2: the angle with the normal of the solvent plane, defined by the same three atoms, or when the option -v23 is set the angle with the vector between atoms 2 and 3.
The reference can be a set of atoms or the center of mass of a set of atoms. The group of solvent atoms should consist of 3 atoms per solvent molecule. Only solvent molecules between -rmin and -rmax are considered for -o and -no each frame.
-o: distribtion of cos(theta1) for rmin=r=rmax.
-no: distribution of cos(theta2) for rmin=r=rmax.
-ro: cos(theta1) and 3cos2(theta2)-1 as a function of the distance.
-co: the sum over all solvent molecules within distance r of cos(theta1) and 3cos2(theta2)-1 as a function of r.
FILES-f traj.xtc Input
-nice int 19
-b time 0
-e time 0
-dt time 0
-rmin real 0
-rmax real 0.5
-cbin real 0.02
-rbin real 0.02