NAME

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

SYNOPSIS

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

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

       -s [<.tpr>] (topol.tpr)
              Portable xdr run input file

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

       Options to specify output files:

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

       Other options:

       -b <time> (0)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit 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 position

       -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

       gmx(1)

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

COPYRIGHT

       2024, GROMACS development team