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

# gmx-dipoles(1)

Compute the total dipole plus fluctuations

## NAME

gmx-dipoles - Compute the total dipole plus fluctuations

## SYNOPSIS

```
gmx dipoles [-en [<.edr>]] [-f [<.xtc/.trr/...>]] [-s [<.tpr>]]
            [-n [<.ndx>]] [-o [<.xvg>]] [-eps [<.xvg>]] [-a [<.xvg>]]
            [-d [<.xvg>]] [-c [<.xvg>]] [-g [<.xvg>]]
            [-adip [<.xvg>]] [-dip3d [<.xvg>]] [-cos [<.xvg>]]
            [-cmap [<.xpm>]] [-slab [<.xvg>]] [-b <time>] [-e <time>]
            [-dt <time>] [-[no]w] [-xvg <enum>] [-mu <real>]
            [-mumax <real>] [-epsilonRF <real>] [-skip <int>]
            [-temp <real>] [-corr <enum>] [-[no]pairs] [-[no]quad]
            [-ncos <int>] [-axis <string>] [-sl <int>]
            [-gkratom <int>] [-gkratom2 <int>] [-rcmax <real>]
            [-[no]phi] [-nlevels <int>] [-ndegrees <int>]
            [-acflen <int>] [-[no]normalize] [-P <enum>]
            [-fitfn <enum>] [-beginfit <real>] [-endfit <real>]
```

## DESCRIPTION

**gmx dipoles** computes the total dipole plus fluctuations of a simulation system. From this you can compute e.g. the dielectric constant for low-dielectric media. For molecules with a net charge, the net charge is subtracted at center of mass of the molecule.

The file **Mtot.xvg** contains the total dipole moment of a frame, the components as well as the norm of the vector. The file **aver.xvg** contains \<\|mu\|^2\> and \|\<mu\>\|^2 during the simulation. The file **dipdist.xvg** contains the distribution of dipole moments during the simulation The value of **-mumax** is used as the highest value in the distribution graph.

Furthermore, the dipole autocorrelation function will be computed when option **-corr** is used. The output file name is given with the **-c** option. The correlation functions can be averaged over all molecules (**mol**), plotted per molecule separately (**molsep**) or it can be computed over the total dipole moment of the simulation box (**total**).

Option **-g** produces a plot of the distance dependent Kirkwood G-factor, as well as the average cosine of the angle between the dipoles as a function of the distance. The plot also includes gOO and hOO according to Nymand & Linse, J. Chem. Phys. 112 (2000) pp 6386-6395. In the same plot, we also include the energy per scale computed by taking the inner product of the dipoles divided by the distance to the third power.

EXAMPLES

**gmx dipoles -corr mol -P 1 -o dip\_sqr -mu 2.273 -mumax 5.0**

This will calculate the autocorrelation function of the molecular dipoles using a first order Legendre polynomial of the angle of the dipole vector and itself a time t later. For this calculation 1001 frames will be used. Further, the dielectric constant will be calculated using an **-epsilonRF** of infinity (default), temperature of 300 K (default) and an average dipole moment of the molecule of 2.273 (SPC). For the distribution function a maximum of 5.0 will be used.

## OPTIONS

Options to specify input files:

- **-en \[\<.edr\>\] (ener.edr) (Optional)**

  Energy file

- **-f \[\<.xtc/.trr/...\>\] (traj.xtc)**

  Trajectory: *xtc* *trr* *cpt* *gro* *g96* *pdb* *tng*

- **-s \[\<.tpr\>\] (topol.tpr)**

  Portable xdr run input file

- **-n \[\<.ndx\>\] (index.ndx) (Optional)**

  Index file

Options to specify output files:

- **-o \[\<.xvg\>\] (Mtot.xvg)**

  xvgr/xmgr file

- **-eps \[\<.xvg\>\] (epsilon.xvg)**

  xvgr/xmgr file

- **-a \[\<.xvg\>\] (aver.xvg)**

  xvgr/xmgr file

- **-d \[\<.xvg\>\] (dipdist.xvg)**

  xvgr/xmgr file

- **-c \[\<.xvg\>\] (dipcorr.xvg) (Optional)**

  xvgr/xmgr file

- **-g \[\<.xvg\>\] (gkr.xvg) (Optional)**

  xvgr/xmgr file

- **-adip \[\<.xvg\>\] (adip.xvg) (Optional)**

  xvgr/xmgr file

- **-dip3d \[\<.xvg\>\] (dip3d.xvg) (Optional)**

  xvgr/xmgr file

- **-cos \[\<.xvg\>\] (cosaver.xvg) (Optional)**

  xvgr/xmgr file

- **-cmap \[\<.xpm\>\] (cmap.xpm) (Optional)**

  X PixMap compatible matrix file

- **-slab \[\<.xvg\>\] (slab.xvg) (Optional)**

  xvgr/xmgr 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

- **-xvg \<enum\> (xmgrace)**

  xvg plot formatting: xmgrace, xmgr, none

- **-mu \<real\> (-1)**

  dipole of a single molecule (in Debye)

- **-mumax \<real\> (5)**

  max dipole in Debye (for histogram)

- **-epsilonRF \<real\> (0)**

  epsilon of the reaction field used during the simulation, needed for dielectric constant calculation. WARNING: 0.0 means infinity (default)

- **-skip \<int\> (0)**

  Skip steps in the output (but not in the computations)

- **-temp \<real\> (300)**

  Average temperature of the simulation (needed for dielectric constant calculation)

- **-corr \<enum\> (none)**

  Correlation function to calculate: none, mol, molsep, total

- **-\[no\]pairs (yes)**

  Calculate \|cos(theta)\| between all pairs of molecules. May be slow

- **-\[no\]quad (no)**

  Take quadrupole into account

- **-ncos \<int\> (1)**

  Must be 1 or 2. Determines whether the \<cos(theta)\> is computed between all molecules in one group, or between molecules in two different groups. This turns on the **-g** flag.

- **-axis \<string\> (Z)**

  Take the normal on the computational box in direction X, Y or Z.

- **-sl \<int\> (10)**

  Divide the box into this number of slices.

- **-gkratom \<int\> (0)**

  Use the n-th atom of a molecule (starting from 1) to calculate the distance between molecules rather than the center of charge (when 0) in the calculation of distance dependent Kirkwood factors

- **-gkratom2 \<int\> (0)**

  Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules

- **-rcmax \<real\> (0)**

  Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterion based on the box length will be used.

- **-\[no\]phi (no)**

  Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the two molecules in the *.xpm* file from the **-cmap** option. By default the cosine of the angle between the dipoles is plotted.

- **-nlevels \<int\> (20)**

  Number of colors in the cmap output

- **-ndegrees \<int\> (90)**

  Number of divisions on the *y*-axis in the cmap output (for 180 degrees)

- **-acflen \<int\> (-1)**

  Length of the ACF, default is half the number of frames

- **-\[no\]normalize (yes)**

  Normalize ACF

- **-P \<enum\> (0)**

  Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3

- **-fitfn \<enum\> (none)**

  Fit function: none, exp, aexp, exp\_exp, exp5, exp7, exp9

- **-beginfit \<real\> (0)**

  Time where to begin the exponential fit of the correlation function

- **-endfit \<real\> (-1)**

  Time where to end the exponential fit of the correlation function, -1 is until the end

## SEE ALSO

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

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

## COPYRIGHT

2025, GROMACS development team