gmx-densorder1
Calculate surface fluctuations
Usage
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>]
Overview
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 |
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.