g_densorder(1) calculate surface fluctuations


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


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


-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 


 Print help info and quit

 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)

 View output  .xvg .xpm .eps and  .pdb files

 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