# gmx dipoles¶

## 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)- 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, 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