NAME
g_potential - calculates the electrostatic potential across the box
VERSION 4.0.1
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 -[no]correct
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
Trajectory: xtc trr trj gro g96 pdb cpt
-n index.ndx Input
Index file
-s topol.tpr Input
Run input file: tpr tpb tpa
-o potential.xvg Output
xvgr/xmgr file
-oc charge.xvg Output
xvgr/xmgr file
-of field.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
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]wno
View output xvg, xpm, eps and pdb files
-[no]xvgryes
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]sphericalno
Calculate spherical thingie
-ng int 1
Number of groups to consider
-[no]correctno
Assume net zero charge of groups to improve accuracy
KNOWN PROBLEMS
- Discarding slices for integration should not be necessary.
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_potential(1)