Provided by: gromacs-data_4.6.5-1build1_all

**NAME**

g_potential - calculates the electrostatic potential across the boxVERSION4.6.5

**SYNOPSIS**

g_potential-ftraj.xtc-nindex.ndx-stopol.tpr-opotential.xvg-occharge.xvg-offield.xvg-[no]h-[no]version-niceint-btime-etime-dttime-[no]w-xvgenum-dstring-slint-cbint-ceint-tzreal-[no]spherical-ngint-[no]correct

**DESCRIPTION**

g_potentialcomputes 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**

-ftraj.xtcInputTrajectory: xtc trr trj gro g96 pdb cpt-nindex.ndxInputIndex file-stopol.tprInputRun input file: tpr tpb tpa-opotential.xvgOutputxvgr/xmgr file-occharge.xvgOutputxvgr/xmgr file-offield.xvgOutputxvgr/xmgr file

**OTHER** **OPTIONS**

-[no]hnoPrint help info and quit-[no]versionnoPrint version info and quit-niceint19Set the nicelevel-btime0First frame (ps) to read from trajectory-etime0Last frame (ps) to read from trajectory-dttime0Only use frame when t MOD dt = first time (ps)-[no]wnoView output.xvg,.xpm,.epsand.pdbfiles-xvgenumxmgracexvg plot formatting:xmgrace,xmgrornone-dstringZTake the normal on the membrane in direction X, Y or Z.-slint10Calculate potential as function of boxlength, dividing the box in this number of slices.-cbint0Discard this number of first slices of box for integration-ceint0Discard this number of last slices of box for integration-tzreal0Translate all coordinates by this distance in the direction of the box-[no]sphericalnoCalculate spherical thingie-ngint1Number of groups to consider-[no]correctnoAssume net zero charge of groups to improve accuracy

**KNOWN** **PROBLEMS**

- Discarding slices for integration should not be necessary.

**SEE** **ALSO**

gromacs(7)More information aboutGROMACSis available at <http://www.gromacs.org/>. Mon 2 Dec 2013 g_potential(1)