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/>.