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]
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.
-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.
-symm symmetrizes the output around the center. This will
automatically turn on
Options to specify input files:
Portable xdr run input file
Options to specify output files:
Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
xvg plot formatting: xmgrace, xmgr, none
Take the normal on the membrane in direction X, Y or Z.
Calculate potential as function of boxlength, dividing the box in this number of slices.
Discard this number of first slices of box for integration
Discard this number of last slices of box for integration
Translate all coordinates by this distance in the direction of the box
Calculate in spherical coordinates
Number of groups to consider
Perform the binning relative to the center of the (changing) box. Useful for bilayers.
Symmetrize the density along the axis, with respect to the center. Useful for bilayers.
Assume net zero charge of groups to improve accuracy
Discarding slices for integration should not be necessary.