gmx densorder


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>]


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 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