.TH gmx-densorder 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-densorder \- Calculate surface fluctuations

.SH SYNOPSIS
gmx densorder [\-s [<.tpr/.tpb/...>]] [\-f [<.xtc/.trr/...>]]
             [\-n [<.ndx>]] [\-o [<.dat>]] [\-or [<.out> [...]]]
             [\-og [<.xpm> [...]]] [\-Spect [<.out> [...]]]
             [\-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>]

.SH DESCRIPTION
\fBgmx densorder\fR reduces 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 \fB\-tavg\fR.

.SH OPTIONS
Options to specify input and output files:

.BI "\-s" " [<.tpr/.tpb/...>] (topol.tpr) (Input)"
    Run input file: tpr tpb tpa

.BI "\-f" " [<.xtc/.trr/...>] (traj.xtc) (Input)"
    Trajectory: xtc trr cpt trj gro g96 pdb tng

.BI "\-n" " [<.ndx>] (index.ndx) (Input)"
    Index file

.BI "\-o" " [<.dat>] (Density4D.dat) (Output, Optional)"
    Generic data file

.BI "\-or" " [<.out> [...]] (hello.out) (Output, Optional)"
    Generic output file

.BI "\-og" " [<.xpm> [...]] (interface.xpm) (Output, Optional)"
    X PixMap compatible matrix file

.BI "\-Spect" " [<.out> [...]] (intfspect.out) (Output, Optional)"
    Generic output file


Other options:

.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: bisect, functional

.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>.