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PROGRAM:

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)
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

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