NAME

       gmx-densorder - Calculate surface fluctuations

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)
              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

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2023, GROMACS development team

2023.3                                            Oct 19, 2023                                  GMX-DENSORDER(1)