g_potential VERSION 3.3_beta_20050823

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

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

-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

-[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.

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.