g_sorient

VERSION 3.1
Thu 28 Feb 2002

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 each frame.

-o: angle distribution of theta1.

-no: angle distribution of theta2.

-ro: <cos(theta1)> and <3cos^2(theta2)-1> as a function of the distance.

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

Files

option	filename	type	description
`-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
`-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

option	type	default	description
`-[no]h`	bool	`no`	Print help info and quit
`-[no]X`	bool	`no`	Use dialog box GUI to edit command line options
`-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`	bool	`no`	View output xvg, xpm, eps and pdb files
`-[no]com`	bool	`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

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