g_densorder - calculate surface fluctuations
VERSION 4.6.3
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
−[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
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