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

# g\_dipoles\_d(1)

Compute the total dipole plus fluctuations

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

## NAME

gmx-dipoles - Compute the total dipole plus fluctuations

## SYNOPSIS

gmx dipoles \[-en \[\<.edr\>\]\] \[-f \[\<.xtc/.trr/...\>\]\]\
             \[-s \[\<.tpr/.tpb/...\>\]\] \[-n \[\<.ndx\>\]\] \[-o \[\<.xvg\>\]\]\
             \[-eps \[\<.xvg\>\]\] \[-a \[\<.xvg\>\]\] \[-d \[\<.xvg\>\]\] \[-c \[\<.xvg\>\]\]\
             \[-g \[\<.xvg\>\]\] \[-adip \[\<.xvg\>\]\] \[-dip3d \[\<.xvg\>\]\]\
             \[-cos \[\<.xvg\>\]\] \[-cmap \[\<.xpm\>\]\] \[-slab \[\<.xvg\>\]\]\
             \[-nice \<int\>\] \[-b \<time\>\] \[-e \<time\>\] \[-dt \<time\>\]\
             \[-\[no\]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 and output files:

**-en** *\[\<.edr\>\] (ener.edr) (Input, Optional)*\
     Energy file

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

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

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

**-o** *\[\<.xvg\>\] (Mtot.xvg) (Output)*\
     xvgr/xmgr file

**-eps** *\[\<.xvg\>\] (epsilon.xvg) (Output)*\
     xvgr/xmgr file

**-a** *\[\<.xvg\>\] (aver.xvg) (Output)*\
     xvgr/xmgr file

**-d** *\[\<.xvg\>\] (dipdist.xvg) (Output)*\
     xvgr/xmgr file

**-c** *\[\<.xvg\>\] (dipcorr.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-g** *\[\<.xvg\>\] (gkr.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-adip** *\[\<.xvg\>\] (adip.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-dip3d** *\[\<.xvg\>\] (dip3d.xvg) (Output, Optional)*\
     xvgr/xmgr file

**-cos** *\[\<.xvg\>\] (cosaver.xvg) (Output, Optional)*\
     xvgr/xmgr file

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

**-slab** *\[\<.xvg\>\] (slab.xvg) (Output, Optional)*\
     xvgr/xmgr file

Other options:

**-nice** *\<int\> (19)*\
     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

**-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, vac, exp5, exp7, exp9, erffit

**-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

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

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