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GMX-DENSORDER(1) GROMACS GMX-DENSORDER(1)

gmx-densorder - Calculate surface fluctuations

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>]


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 files:

Portable xdr run input file
Trajectory: xtc trr cpt gro g96 pdb tng
Index file

Options to specify output files:

Generic data file
Generic output file
X PixMap compatible matrix file
Generic output file

Other options:

Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
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
Binwidth of density distribution tangential to interface
Binwidth of density distribution normal to interface
Order of Gaussian filter, order 0 equates to NO filtering
Axis Direction - X, Y or Z
Interface location method: bisect, functional
Bulk density phase 1 (at small z)
Bulk density phase 2 (at large z)
Number of frames in one time-block average
Number of Height levels in 2D - XPixMaps

gmx(1)

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2023, GROMACS development team

February 3, 2023 2022.5