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GMX-POTENTIAL(1)		     GROMACS			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]center]
		     [-[no]symm] [-[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 in-
     tegrating 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  coor-
     dinates  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.

     Option  -center  performs	the  histogram binning and potential calculation
     relative to the center of an arbitrary group, in absolute box  coordinates.
     If  you  are calculating profiles along the Z axis box dimension bZ, output
     would be from -bZ/2 to bZ/2 if you center based on the entire system.   Op-
     tion  -symm  symmetrizes  the output around the center. This will automati-
     cally turn on -center too.

OPTIONS
     Options to specify input files:

     -f [<.xtc/.trr/...>] (traj.xtc)
	    Trajectory: xtc trr cpt gro g96 pdb tng h5md

     -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)
	    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

     -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 in spherical coordinates

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

     -[no]center (no)
	    Perform the binning relative to the center of  the	(changing)  box.
	    Useful for bilayers.

     -[no]symm (no)
	    Symmetrize	the  density along the axis, with respect to the center.
	    Useful for bilayers.

     -[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
     2026, GROMACS development team

2026.3				  Jun 25, 2026			GMX-POTENTIAL(1)
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