Main Table of Contents

Fri 5 Jul 2013


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:

θ_1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3.
θ_2: 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(θ_1) for rmin<=r<=rmax.

-no: distribution of cos(θ_2) for rmin<=r<=rmax.

-ro: and <3cos(^2θ_2)-1> as a function of the distance.

-co: the sum over all solvent molecules within distance r of cos(θ_1) and 3cos(^2(θ_2)-1) as a function of r.

-rc: the distribution of the solvent molecules as a function of r


-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb
-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
-rc scount.xvg Output xvgr/xmgr file

Other options

-[no]h bool no Print help info and quit
-[no]version bool no Print version 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 bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]com bool no Use the center of mass as the reference postion
-[no]v23 bool no Use the vector between atoms 2 and 3
-rmin real 0 Minimum distance (nm)
-rmax real 0.5 Maximum distance (nm)
-cbin real 0.02 Binwidth for the cosine
-rbin real 0.02 Binwidth for r (nm)
-[no]pbc bool no Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.