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g_potential(1) [debian man page]

g_potential(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				    g_potential(1)

NAME

       g_potential - calculates the electrostatic potential across the box

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_potential  -f	traj.xtc  -n index.ndx -s topol.tpr -o potential.xvg -oc charge.xvg -of field.xvg -[no]h -[no]version -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

	g_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
       distribution in spherical slices and twice integrating them. epsilon_r is taken as 1, but 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

       -[no]versionno
	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]wno
	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]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/>.

								  Mon 4 Apr 2011						    g_potential(1)

Check Out this Related Man Page

g_mdmat(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					g_mdmat(1)

NAME

       g_mdmat - calculates residue contact maps

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_mdmat	-f  traj.xtc  -s topol.tpr -n index.ndx -mean dm.xpm -frames dmf.xpm -no num.xvg -[no]h -[no]version -nice int -b time -e time -dt
       time -xvg enum -t real -nlevels int

DESCRIPTION

	g_mdmat makes distance matrices consisting of the smallest distance between residue pairs. With  -frames, these distance matrices  can	be
       stored  in  order  to see differences in tertiary structure as a function of time. If you choose your options unwisely, this may generate a
       large output file. By default, only an averaged matrix over the whole trajectory is output.  Also a count of the number of different atomic
       contacts between residues over the whole trajectory can be made.  The output can be processed with  xpm2ps to make a PostScript (tm) plot.

FILES

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
	Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
	Index file

       -mean dm.xpm Output
	X PixMap compatible matrix file

       -frames dmf.xpm Output, Opt.
	X PixMap compatible matrix file

       -no num.xvg Output, Opt.
	xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	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)

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -t real 1.5
	trunc distance

       -nlevels int 40
	Discretize distance in	levels

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011							g_mdmat(1)
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