NAME

       g_spol - analyzes solvent dipole orientation and polarization around solutes

       VERSION 4.6.5

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
       distances is plotted.  For each distance between  -rmin and  -rmax the  inner  product  of  the  distance
       vector  and  the  dipole  of  the  solvent molecule 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 2 Dec 2013                                        g_spol(1)