g_density(1) [debian man page]

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

NAME

       g_density - calculates the density of the system

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_density  -f  traj.xtc	-n  index.ndx -s topol.tpr -ei electrons.dat -o density.xvg -[no]h -[no]version -nice int -b time -e time -dt time
       -[no]w -xvg enum -d string -sl int -dens enum -ng int -[no]symm -[no]center

DESCRIPTION

       Compute partial densities across the box, using an index file.

       For the total density of NPT simulations, use  g_energy instead.

       Densities are in kg/m3, and number densities or electron densities can also be calculated. For electron densities, a  file  describing  the
       number of electrons for each type of atom should be provided using  -ei.  It should look like:

	   2

	   atomname = nrelectrons

	   atomname = nrelectrons

       The first line contains the number of lines to read from the file.  There should be one line for each unique atom name in your system.  The
       number of electrons for each atom is modified by its atomic partial charge.

FILES

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

       -n index.ndx Input, Opt.
	Index file

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

       -ei electrons.dat Input, Opt.
	Generic data file

       -o density.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 50
	Divide the box in nr slices.

       -dens enum mass
	Density:  mass,  number,  charge or  electron

       -ng int 1
	Number of groups to compute densities of

       -[no]symmno
	Symmetrize the density along the axis, with respect to the center. Useful for bilayers.

       -[no]centerno
	Shift the center of mass along the axis to zero. This means if your axis is Z and your box is bX, bY, bZ, the center of mass  will  be	at
       bX/2, bY/2, 0.

KNOWN PROBLEMS

       - When calculating electron densities, atomnames are used instead of types. This is bad.

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						      g_density(1)

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)