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g_densorder

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

NAME

       g_densorder - calculate surface fluctuations

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_densorder -s topol.tpr -f traj.xtc -n index.ndx -o Density4D.dat -or hello.out -og interface.xpm -Spect intfspect.out -[no]h -[no]version
       -nice int -b time -e time -dt time -[no]w -[no]1d -bw real -bwn real -order int -axis string -method enum -d1 real  -d2	real  -tblock  int
       -nlevel int

DESCRIPTION

       A small program to reduce a two-phase density distribution along an axis, computed over a MD trajectory to 2D surfaces fluctuating in time,
       by a fit to a functional profile for interfacial densities A time-averaged spatial representation of the interfaces can be output with  the
       option -tavg

FILES

       -s topol.tpr Input
	Run input file: tpr tpb tpa

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

       -n index.ndx Input
	Index file

       -o Density4D.dat Output, Opt.
	Generic data file

       -or hello.out Output, Opt., Mult.
	Generic output file

       -og interface.xpm Output, Opt., Mult.
	X PixMap compatible matrix file

       -Spect intfspect.out Output, Opt., Mult.
	Generic output file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 0
	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

       -[no]1dno
	Pseudo-1d interface geometry

       -bw real 0.2
	Binwidth of density distribution tangential to interface

       -bwn real 0.05
	Binwidth of density distribution normal to interface

       -order int 0
	Order of Gaussian filter, order 0 equates to NO filtering

       -axis string Z
	Axis Direction - X, Y or Z

       -method enum bisect
	Interface location method:  bisect or  functional

       -d1 real 0
	Bulk density phase 1 (at small z)

       -d2 real 1000
	Bulk density phase 2 (at large z)

       -tblock int 100
	Number of frames in one time-block average

       -nlevel int 100
	Number of Height levels in 2D - XPixMaps

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						    g_densorder(1)