NAME

       g_potential - calculates the electrostatic potential across the box

       VERSION 4.6.5

SYNOPSIS

       g_potential  -f  traj.xtc  -n  index.ndx  -s topol.tpr -o potential.xvg -oc charge.xvg -of
       field.xvg -[no]h -[no]version -nice int -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

         g_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.

FILES

       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -n index.ndx Input
        Index file

       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -o potential.xvg Output
        xvgr/xmgr file

       -oc charge.xvg Output
        xvgr/xmgr file

       -of field.xvg Output
        xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version 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)

       -[no]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  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]sphericalno
        Calculate spherical thingie

       -ng int 1
        Number of groups to consider

       -[no]correctno
        Assume net zero charge of groups to improve accuracy

KNOWN PROBLEMS

       - Discarding slices for integration should not be necessary.

SEE ALSO

       gromacs(7)

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

                                          Mon 2 Dec 2013                           g_potential(1)