g_sorient

Main Table of Contents

VERSION 4.5
Thu 26 Aug 2010


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, 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 <3cos^2(theta2)-1> as a function of the distance.

-co: the sum over all solvent molecules within distance r of cos(theta1) and 3cos^2(theta2)-1 as a function of r.

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

Files

optionfilenametypedescription
-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

optiontypedefaultdescription
-[no]h gmx_bool no Print help info and quit
-[no]version gmx_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 gmx_bool no View output xvg, xpm, eps and pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]com gmx_bool no Use the center of mass as the reference postion
-[no]v23 gmx_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 gmx_bool no Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.


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