**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 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