Synopsis
gmx densorder [-s [<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
[-o [<.dat>]] [-or [<.out> [...]]] [-og [<.xpm> [...]]]
[-Spect [<.out> [...]]] [-nice ] [-b ] [-e ]
[-dt ] [-[no]w] [-[no]1d] [-bw ] [-bwn ]
[-order ] [-axis ] [-method ] [-d1 ]
[-d2 ] [-tblock ] [-nlevel ]
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
Generic output file
-og xpm > [...]] (interface.xpm ) (Output, Optional)
X PixMap compatible matrix file
-Spect
Generic output file
Other options:
-nice
Set the nicelevel
-b
First frame (ps) to read from trajectory
-e
Last frame (ps) to read from trajectory
-dt
Only use frame when t MOD dt = first time (ps)
-[no]w
View output .xvg , .xpm , .eps and .pdb files
-[no]1d
Pseudo-1d interface geometry
-bw
Binwidth of density distribution tangential to interface
-bwn
Binwidth of density distribution normal to interface
-order
Order of Gaussian filter, order 0 equates to NO filtering
-axis
Axis Direction - X, Y or Z
-method
Interface location method: bisect, functional
-d1
Bulk density phase 1 (at small z)
-d2
Bulk density phase 2 (at large z)
-tblock
Number of frames in one time-block average
-nlevel
Number of Height levels in 2D - XPixMaps
