---
name: "gmx-densorder"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2025.2-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-densorder"
---

# gmx-densorder(1)

Calculate surface fluctuations

## 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)](/gmx/1.md)**

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

## COPYRIGHT

2025, GROMACS development team