.TH g_densorder 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_densorder - calculate surface fluctuations

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_densorder\fP
.BI "\-s" " topol.tpr "
.BI "\-f" " traj.xtc "
.BI "\-n" " index.ndx "
.BI "\-o" " Density4D.dat "
.BI "\-or" " hello.out "
.BI "\-og" " interface.xpm "
.BI "\-Spect" " intfspect.out "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-[no]1d" ""
.BI "\-bw" " real "
.BI "\-bwn" " real "
.BI "\-order" " int "
.BI "\-axis" " string "
.BI "\-method" " enum "
.BI "\-d1" " real "
.BI "\-d2" " real "
.BI "\-tblock" " int "
.BI "\-nlevel" " int "
.SH 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
.SH FILES
.BI "\-s" " topol.tpr" 
.B Input
 Run input file: tpr tpb tpa 

.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-n" " index.ndx" 
.B Input
 Index file 

.BI "\-o" " Density4D.dat" 
.B Output, Opt.
 Generic data file 

.BI "\-or" " hello.out" 
.B Output, Opt., Mult.
 Generic output file 

.BI "\-og" " interface.xpm" 
.B Output, Opt., Mult.
 X PixMap compatible matrix file 

.BI "\-Spect" " intfspect.out" 
.B Output, Opt., Mult.
 Generic output file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 0" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-[no]1d"  "no    "
 Pseudo\-1d interface geometry

.BI "\-bw"  " real" " 0.2   " 
 Binwidth of density distribution tangential to interface

.BI "\-bwn"  " real" " 0.05  " 
 Binwidth of density distribution normal to interface

.BI "\-order"  " int" " 0" 
 Order of Gaussian filter, order 0 equates to NO filtering

.BI "\-axis"  " string" " Z" 
 Axis Direction \- X, Y or Z

.BI "\-method"  " enum" " bisect" 
 Interface location method: \fB bisect\fR or \fB functional\fR

.BI "\-d1"  " real" " 0     " 
 Bulk density phase 1 (at small z)

.BI "\-d2"  " real" " 1000  " 
 Bulk density phase 2 (at large z)

.BI "\-tblock"  " int" " 100" 
 Number of frames in one time\-block average

.BI "\-nlevel"  " int" " 100" 
 Number of Height levels in 2D \- XPixMaps

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.