debian man page for g_potential

g_potential(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				    g_potential(1)

NAME
       g_potential - calculates the electrostatic potential across the box

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS
       g_potential  -f	traj.xtc  -n index.ndx -s topol.tpr -o potential.xvg -oc charge.xvg -of field.xvg -[no]h -[no]version -nice int -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
	g_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.

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

       -[no]versionno
	Print version 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

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  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 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/>.

								  Mon 4 Apr 2011						    g_potential(1)