Man Linux: Main Page and Category List


       g_spol  -  analyzes  solvent dipole orientation and polarization around

       VERSION 4.0.1


       g_spol -f traj.xtc -s topol.tpr -n index.ndx -o scdist.xvg -[no]h -nice
       int -b time -e time -dt time -[no]w -[no]xvgr -[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.  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

       -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

        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

        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

                                Thu 16 Oct 2008                      g_spol(1)