g_sgangle(1) [debian man page]

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

NAME

       g_sgangle - computes the angle and distance between two groups

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_sgangle  -f  traj.xtc	-n index.ndx -s topol.tpr -oa sg_angle.xvg -od sg_dist.xvg -od1 sg_dist1.xvg -od2 sg_dist2.xvg -[no]h -[no]version
       -nice int -b time -e time -dt time -[no]w -xvg enum -[no]one -[no]z

DESCRIPTION

       Compute the angle and distance between two groups.  The groups are defined by a number of atoms given in an index file and may  be  two	or
       three  atoms in size.  If  -one is set, only one group should be specified in the index file and the angle between this group at time 0 and
       t will be computed.  The angles calculated depend on the order in which the atoms are given. Giving, for instance, 5 6 will rotate the vec-
       tor 5-6 with 180 degrees compared to giving 6 5.

       If three atoms are given, the normal on the plane spanned by those three atoms will be calculated, using the formula  P1P2 x P1P3.  The cos
       of the angle is calculated, using the inproduct of the two normalized vectors.

       Here is what some of the file options do:

	-oa: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane	defined  by  those
       three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used.

	-od: Distance between two groups. Distance is taken from the center of one group to the center of the other group.

	-od1: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given separately.

	-od2: For two planes this option has no meaning.

FILES

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

       -n index.ndx Input
	Index file

       -s topol.tpr Input
	Run input file: tpr tpb tpa

       -oa sg_angle.xvg Output
	xvgr/xmgr file

       -od sg_dist.xvg Output, Opt.
	xvgr/xmgr file

       -od1 sg_dist1.xvg Output, Opt.
	xvgr/xmgr file

       -od2 sg_dist2.xvg Output, Opt.
	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]oneno
	Only one group compute angle between vector at time zero and time t

       -[no]zno
	Use the  z-axis as reference

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						      g_sgangle(1)

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)