g_densorder(1) - Linux man page

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 -niceint -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

-stopol.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