g_sorient

VERSION 4.6.1
Tue 5 Mar 2013

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:

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

Files

option	filename	type	description
`-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

option	type	default	description
`-[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.

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