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gmx-densorder(1)                GROMACS Manual                gmx-densorder(1)

NAME
       gmx-densorder - Calculate surface fluctuations

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>]

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 and output files:

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

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

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

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

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

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

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

       Other options:

       -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  (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
       gromacs(7)

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

VERSION 5.0.6                                                 gmx-densorder(1)