g_potential_d (1) Linux Manual Page

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/>.