Provided by: gromacs-data_4.6.5-1build1_all bug


       g_spol - analyzes solvent dipole orientation and polarization around solutes

       VERSION 4.6.5


       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


        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.


       -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


        Print help info and quit

        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)

        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

        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



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                                g_spol(1)