Main Table of Contents

Fri 5 Jul 2013


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

Other options

-[no]h bool no Print help info and quit
-[no]version bool no 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]w bool no View output .xvg, .xpm, .eps and .pdb files
-[no]1d bool no 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