Man page - gmx-densorder(1)
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apt-get install gromacs-data
Manual
GMX-DENSORDER
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
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)
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2025, GROMACS development team