debian man page for g_spol

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)