---
name: "g_densorder"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "5.0.2-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-densorder"
---

# g\_densorder(1)

Calculate surface fluctuations

Part of [gmx-densorder(1)](/gmx-densorder/1.md).

## NAME

gmx-densorder - Calculate surface fluctuations

## SYNOPSIS

gmx densorder \[-s \[\<.tpr/.tpb/...\>\]\] \[-f \[\<.xtc/.trr/...\>\]\]\
              \[-n \[\<.ndx\>\]\] \[-o \[\<.dat\>\]\] \[-or \[\<.out\> \[...\]\]\]\
              \[-og \[\<.xpm\> \[...\]\]\] \[-Spect \[\<.out\> \[...\]\]\]\
              \[-nice \<int\>\] \[-b \<time\>\] \[-e \<time\>\] \[-dt \<time\>\]\
              \[-\[no\]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 and output files:

**-s** *\[\<.tpr/.tpb/...\>\] (topol.tpr) (Input)*\
     Run input file: tpr tpb tpa

**-f** *\[\<.xtc/.trr/...\>\] (traj.xtc) (Input)*\
     Trajectory: xtc trr cpt trj gro g96 pdb tng

**-n** *\[\<.ndx\>\] (index.ndx) (Input)*\
     Index file

**-o** *\[\<.dat\>\] (Density4D.dat) (Output, Optional)*\
     Generic data file

**-or** *\[\<.out\> \[...\]\] (hello.out) (Output, Optional)*\
     Generic output file

**-og** *\[\<.xpm\> \[...\]\] (interface.xpm) (Output, Optional)*\
     X PixMap compatible matrix file

**-Spect** *\[\<.out\> \[...\]\] (intfspect.out) (Output, Optional)*\
     Generic output file

Other options:

**-nice** *\<int\> (0)*\
     Set the nicelevel

**-b** *\<time\> (0)*\
     First frame (ps) to read from trajectory

**-e** *\<time\> (0)*\
     Last frame (ps) to read from trajectory

**-dt** *\<time\> (0)*\
     Only use frame when t MOD dt = first time (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

**[gromacs(7)](/gromacs/7.md)**

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