Provided by: gromacs-data_2019.3-2_all bug

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)
              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]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

       2019, GROMACS development team