Login or Register to Ask a Question and Join Our Community

Linux and UNIX Man Pages

Linux & Unix Commands - Search Man Pages

g_spol(1) [debian man page]

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

NAME

       g_spol - analyzes solvent dipole orientation and polarization around solutes

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_spol -f traj.xtc -s topol.tpr -n index.ndx -o scdist.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]com
       -refat int -rmin real -rmax real -dip real -bw real

DESCRIPTION

	g_spol analyzes dipoles around a solute; it is especially useful for polarizable water. A group of reference atoms, or a  center  of  mass
       reference  (option   -com) and a group of solvent atoms is required. The program splits the group of solvent atoms into molecules. For each
       solvent molecule the distance to the closest atom in reference group or to the COM is determined.  A cumulative distribution of these  dis-
       tances is plotted.  For each distance between  -rmin and  -rmax the inner product of the distance vector and the dipole of the solvent mol-
       ecule is determined.  For solvent molecules with net charge (ions), the net charge of the ion is subtracted evenly from all  atoms  in  the
       selection of each ion.  The average of these dipole components is printed.  The same is done for the polarization, where the average dipole
       is subtracted from the instantaneous dipole. The magnitude of the average dipole is set with the option	-dip, the direction is defined	by
       the vector from the first atom in the selected solvent group to the midpoint between the second and the third atom.

FILES

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

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

       -n index.ndx Input, Opt.
	Index file

       -o scdist.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

       -refat int 1
	The reference atom of the solvent molecule

       -rmin real 0
	Maximum distance (nm)

       -rmax real 0.32
	Maximum distance (nm)

       -dip real 0
	The average dipole (D)

       -bw real 0.01
	The bin width

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011							 g_spol(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)
Man Page