g_sorient(1)

NAME
g_sorient VERSION 3.2.0

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]com -rmin real -rmax real -nbin int -[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 : angle distribution of theta1. -no : angle distribution of theta2. -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 -1
 First frame (ps) to read from trajectory -e time -1
 Last frame (ps) to read from trajectory -dt time -1
 Only use frame when t MOD dt = first time (ps) -[no]w no
 View output xvg, xpm, eps and pdb files -[no]com no
 Use the center of mass as the reference postion -rmin real 0
 Minimum distance -rmax real 0.5
 Maximum distance -nbin int 20
 Number of bins -[no]pbc no
 Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.