gmx-potential man page on DragonFly

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gmx-potential(1)		GROMACS Manual		      gmx-potential(1)

NAME
       gmx-potential - Calculate the electrostatic potential across the box

SYNOPSIS
       gmx potential [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
		    [-s [<.tpr/.tpb/...>]] [-o [<.xvg>]] [-oc [<.xvg>]]
		    [-of [<.xvg>]] [-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]correct]

DESCRIPTION
       gmx  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  distri‐
       bution  in  spherical  slices  and twice integrating them. epsilon_r is
       taken as 1, but 2 is more appropriate in many cases.

OPTIONS
       Options to specify input and output files:

       -f [<.xtc/.trr/...>] (traj.xtc) (Input)
	   Trajectory: xtc trr cpt trj gro g96 pdb tng

       -n [<.ndx>] (index.ndx) (Input)
	   Index file

       -s [<.tpr/.tpb/...>] (topol.tpr) (Input)
	   Run input file: tpr tpb tpa

       -o [<.xvg>] (potential.xvg) (Output)
	   xvgr/xmgr file

       -oc [<.xvg>] (charge.xvg) (Output)
	   xvgr/xmgr file

       -of [<.xvg>] (field.xvg) (Output)
	   xvgr/xmgr file

       Other options:

       -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

       -xvg <enum> (xmgrace)
	   xvg plot formatting: xmgrace, xmgr, 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
       this number of slices.

       -cb <int> (0)
	   Discard this number of  first slices of box for integration

       -ce <int> (0)
	   Discard this number of last slices of box for integration

       -tz <real> (0)
	   Translate  all coordinates by this distance in the direction of the
       box

       -[no]spherical  (no)
	   Calculate spherical thingie

       -ng <int> (1)
	   Number of groups to consider

       -[no]correct  (no)
	   Assume net zero charge of groups to improve accuracy

KNOWN ISSUES
       - Discarding slices for integration should not be necessary.

SEE ALSO
       gromacs(7)

       More  information  about	 GROMACS  is  available	 at   <http://www.gro‐
       macs.org/>.

VERSION 5.0.6						      gmx-potential(1)

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