gmx densorder
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