table of contents
g_potential(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_potential(1) |
NAME¶
g_potential - calculates the electrostatic potential across the boxSYNOPSIS¶
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]correctDESCRIPTION¶
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 InputTrajectory: xtc trr trj gro g96 pdb cpt
Index file
Run input file: tpr tpb tpa
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Take the normal on the membrane in direction X, Y or Z.
Calculate potential as function of boxlength, dividing the box in nr slices.
Discard first nr slices of box for integration
Discard last nr slices of box for integration
Translate all coordinates distance in the direction of the box
Calculate spherical thingie
Number of groups to consider
Assume net zero charge of groups to improve accuracy
KNOWN PROBLEMS¶
- Discarding slices for integration should not be necessary.SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |