g_potential(1)
NAME
g_potential - calculates the electrostatic potential across the box
SYNOPSIS
g_potential -f traj.xtc -n index.ndx -s topol.tpr -o potential.xvg -oc charge.xvg -of field.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -d string -sl int -cb int -ce int -tz real -[no]spherical -ng int
DESCRIPTION
Compute the electrostatical potential across the box. The potential
iscalculated by first summing the charges per slice and then integratingtwice of this charge distribution. Periodic boundaries are not taken
into account. Reference of potential is taken to be the left side ofthe
box. It's also possible to calculate the potential in sphericalcoordinates as function of r by calculating a charge distribution inspherical
slices and twice integrating them. epsilon_r is taken as 1,2 is more
appropriate in many cases
FILES
- -f traj.xtc Input
- Generic trajectory: xtc trr trj gro g96 pdb
- -n index.ndx Input
- Index file
- -s topol.tpr Input
- Generic run input: tpr tpb tpa xml
- -o potential.xvg Output
- xvgr/xmgr file
- -oc charge.xvg Output
- xvgr/xmgr file
- -of field.xvg Output
- xvgr/xmgr file
OTHER OPTIONS
- -[no]h no
- Print help info and quit
- -nice int 19
- Set the nicelevel
- -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
- -[no]xvgr yes
- Add specific codes (legends etc.) in the output xvg files for the
- xmgrace program
- -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 nr
- slices.
- -cb int 0
- Discard first nr slices of box for integration
- -ce int 0
- Discard last nr slices of box for integration
- -tz real 0
- Translate all coordinates distance in the direction of the box
- -[no]spherical no
- Calculate spherical thingie
- -ng int 1
- Number of groups to consider
- - Discarding slices for integration should not be necessary.
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.