debian man page for g_sorient

g_sorient(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_sorient(1)

NAME
       g_sorient - analyzes solvent orientation around solutes

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS
       g_sorient -f traj.xtc -s topol.tpr -n index.ndx -o sori.xvg -no snor.xvg -ro sord.xvg -co scum.xvg -rc scount.xvg -[no]h -[no]version -nice
       int -b time -e time -dt time -[no]w -xvg enum -[no]com -[no]v23 -rmin real -rmax real -cbin real -rbin real -[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, 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  sol-
       vent 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 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.

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

FILES
       -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]hno
	Print help info and quit

       -[no]versionno
	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]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -[no]comno
	Use the center of mass as the reference postion

       -[no]v23no
	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]pbcno
	Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.

SEE ALSO
       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						      g_sorient(1)