gmx-densorder - Calculate surface fluctuations

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                  GMX-DENSORDER(1)

gmxdensorder  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.

       gmx-densorder - Calculate surface fluctuations

       Options to specify input files:

       -s[<.tpr>](topol.tpr)
              Portable xdr run input file

       -f[<.xtc/.trr/...>](traj.xtc)
              Trajectory: xtctrrcptgrog96pdbtng-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

gmx(1)

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

          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>]