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gmx-spol(1)                     GROMACS Manual                     gmx-spol(1)

NAME
       gmx-spol - Analyze solvent dipole orientation and polarization around
       solutes

SYNOPSIS
       gmx spol [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
                [-o [<.xvg>]] [-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
       gmx 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.

OPTIONS
       Options to specify input and output files:

       -f [<.xtc/.trr/...>] (traj.xtc) (Input)
           Trajectory: xtc trr cpt trj gro g96 pdb tng

       -s [<.tpr/.tpb/...>] (topol.tpr) (Input)
           Run input file: tpr tpb tpa

       -n [<.ndx>] (index.ndx) (Input, Optional)
           Index file

       -o [<.xvg>] (scdist.xvg) (Output)
           xvgr/xmgr file

       Other options:

       -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]w  (no)
           View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum> (xmgrace)
           xvg plot formatting: xmgrace, xmgr, none

       -[no]com  (no)
           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/>.

VERSION 5.0.6                                                      gmx-spol(1)