xenial (1) gmx-potential.1.gz

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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>
              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/>.


       2015, GROMACS development team