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GMX-DENSORDER(1)		    GROMACS		      GMX-DENSORDER(1)

NAME
       gmx-densorder - Calculate surface fluctuations

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

OPTIONS
       Options to specify input	files:

       -s [<.tpr>] (topol.tpr)
	      Portable xdr run input file

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

       -n [<.ndx>] (index.ndx)
	      Index file

       Options to specify output files:

       -o [<.dat>] (Density4D.dat) (Optional)
	      Generic data file

       -or [<.out> [...]] (hello.out) (Optional)
	      Generic output file

       -og [<.xpm> [...]] (interface.xpm) (Optional)
	      X	PixMap compatible matrix file

       -Spect [<.out> [...]] (intfspect.out) (Optional)
	      Generic output file

       Other options:

       -b <time> (0)
	      Time of first frame to read from trajectory (default unit	ps)

       -e <time> (0)
	      Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
	      Only use frame when t MOD	dt = first time	(default unit ps)

       -[no]w (no)
	      View output .xvg,	.xpm, .eps and .pdb files

       -[no]1d (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, 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

SEE ALSO
       gmx(1)

       More	information    about	GROMACS	   is	 available    at    <-
       http://www.gromacs.org/>.

COPYRIGHT
       2025, GROMACS development team

2025.0				 Feb 10, 2025		      GMX-DENSORDER(1)

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