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