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 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.

       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.  Option  -symm
       symmetrizes the output around the center. This will automatically turn on -center too.

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)
              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

       2023, GROMACS development team

2023.3                                            Oct 19, 2023                                  GMX-POTENTIAL(1)