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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)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | KNOWN ISSUES | SEE ALSO

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