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

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                       GMX-SPOL(1)

gmxspol  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.

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

       Options to specify input files:

       -f[<.xtc/.trr/...>](traj.xtc)
              Trajectory: xtctrrcptgrog96pdbtng-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

gmx(1)

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

          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>]