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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)

Check Out this Related Man Page

g_h2order(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_h2order(1)

NAME

       g_h2order - computes the orientation of water molecules

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_h2order  -f  traj.xtc	-n index.ndx -nm index.ndx -s topol.tpr -o order.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w
       -xvg enum -d string -sl int

DESCRIPTION

	g_h2order computes the orientation of water molecules with respect to the normal of the box. The program determines the average cosine	of
       the  angle between the dipole moment of water and an axis of the box. The box is divided in slices and the average orientation per slice is
       printed.  Each water molecule is assigned to a slice, per time frame, based on the position of the oxygen. When	-nm  is  used,	the  angle
       between the water dipole and the axis from the center of mass to the oxygen is calculated instead of the angle between the dipole and a box
       axis.

FILES

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

       -n index.ndx Input
	Index file

       -nm index.ndx Input, Opt.
	Index file

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

       -o order.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

       -d string Z
	Take the normal on the membrane in direction X, Y or Z.

       -sl int 0
	Calculate order parameter as function of boxlength, dividing the box in nr slices.

KNOWN PROBLEMS

       - The program assigns whole water molecules to a slice, based on the first atom of three in the index  file  group.  It	assumes  an  order
       O,H,H. Name is not important, but the order is. If this demand is not met, assigning molecules to slices is different.

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						      g_h2order(1)
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