## g_densorder

Main Table of Contents

VERSION 4.6
Sat 19 Jan 2013

### 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

option | filename | type | description
--- | --- | --- | ---
`-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

option | type | default | description
--- | --- | --- | ---
`-[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

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