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gmx-potential(1)


NAME

   gmx-potential - Calculate the electrostatic potential across the box

SYNOPSIS

      gmx potential [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-s [<.tpr>]]
                   [-o [<.xvg>]] [-oc [<.xvg>]] [-of [<.xvg>]] [-b <time>]
                   [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>]
                   [-d <string>] [-sl <int>] [-cb <int>] [-ce <int>]
                   [-tz <real>] [-[no]spherical] [-ng <int>] [-[no]correct]

DESCRIPTION

   gmx  potential  computes  the electrostatical potential across the box.
   The potential is calculated by first summing the charges per slice  and
   then integrating twice of this charge distribution. Periodic boundaries
   are not taken into account. Reference of potential is taken to  be  the
   left side of the box. It is also possible to calculate the potential in
   spherical  coordinates  as  function  of  r  by  calculating  a  charge
   distribution  in spherical slices and twice integrating them. epsilon_r
   is taken as 1, but 2 is more appropriate in many cases.

OPTIONS

   Options to specify input files:

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

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

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

   Options to specify output files:

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

   -oc [<.xvg>] (charge.xvg)
          xvgr/xmgr file

   -of [<.xvg>] (field.xvg)
          xvgr/xmgr file

   Other options:

   -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

   -d <string> (Z)
          Take the normal on the membrane in direction X, Y or Z.

   -sl <int> (10)
          Calculate potential as function of boxlength, dividing  the  box
          in this number of slices.

   -cb <int> (0)
          Discard this number of  first slices of box for integration

   -ce <int> (0)
          Discard this number of last slices of box for integration

   -tz <real> (0)
          Translate  all  coordinates by this distance in the direction of
          the box

   -[no]spherical (no)
          Calculate spherical thingie

   -ng <int> (1)
          Number of groups to consider

   -[no]correct (no)
          Assume net zero charge of groups to improve accuracy

KNOWN ISSUES

   * Discarding slices for integration should not be necessary.

SEE ALSO

   gmx(1)

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

COPYRIGHT

   2016, GROMACS development team



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