Main Table of Contents

Thu 26 Aug 2010


Compute 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's 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, 2 is more appropriate in many cases.


-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]h gmx_bool no Print help info and quit
-[no]version gmx_bool no 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]w gmx_bool no 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]spherical gmx_bool no Calculate spherical thingie
-ng int 1 Number of groups to consider
-[no]correct gmx_bool no Assume net zero charge of groups to improve accuracy

Known problems