GMX-DENSORDER(1) GROMACS GMX-DENSORDER(1) 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, com- puted 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 h5md -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 2026, GROMACS development team 2026.3 Jun 25, 2026 GMX-DENSORDER(1)
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