man g_sorient (Commandes) - g_sorient VERSION 3.3_beta_20050823
NAME
g_sorient VERSION 3.3_beta_20050823
SYNOPSIS
g_sorient -f traj.xtc -s topol.tpr -n index.ndx -o sori.xvg -no snor.xvg -ro sord.xvg -co scum.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]com -rmin real -rmax real -bin real -[no]pbc
DESCRIPTION
g_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.
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 3cos2(theta2)-1 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 Generic trajectory: xtc trr trj gro g96 pdb
-s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-n index.ndx Input, Opt. Index file
-o sori.xvg Output xvgr/xmgr file
-no snor.xvg Output xvgr/xmgr file
-ro sord.xvg Output xvgr/xmgr file
-co scum.xvg Output xvgr/xmgr file
OTHER OPTIONS
-[no]h no Print help 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)
-[no]w no View output xvg, xpm, eps and pdb files
-[no]xvgr yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-[no]com no Use the center of mass as the reference postion
-rmin real 0 Minimum distance
-rmax real 0.5 Maximum distance
-bin real 0.02 Binwidth
-[no]pbc no Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.