gmx-densorder (1)

gmx densorder [-s [<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]]

             [-n [<.ndx>]] [-o [<.dat>]] [-or [<.out> [...]]]
             [-og [<.xpm> [...]]] [-Spect [<.out> [...]]]
             [-nice <int>] [-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 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 [<.out> [...]] (hello.out) (Output, Optional)

    Generic output file

-og [<.xpm> [...]] (interface.xpm) (Output, Optional)

    X PixMap compatible matrix file

-Spect [<.out> [...]] (intfspect.out) (Output, Optional)

    Generic output file

Other options:

-nice <int> (0)

    Set the nicelevel

-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

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.