4.9.4. Dielectric — MDAnalysis.analysis.dielectric

Authors:

Mattia Felice Palermo, Philip Loche

Year:

2022

Copyright:

GNU Public License v3

class MDAnalysis.analysis.dielectric.DielectricConstant(atomgroup, temperature=300, make_whole=True, **kwargs)[source]

Computes the average dipole moment

\[\boldsymbol M = \sum_i q_i \boldsymbol r_i\]

where \(q_i\) is the charge and \(\boldsymbol r_i\) the position of atom \(i\) in the given MDAnalysis.core.groups.AtomGroup. Also, the static dielectric constant

\[\varepsilon = 1 + \frac{\langle M^2 \rangle - \langle M \rangle^2} {3 \varepsilon_ 0 V k_B T}\]

is calculated for a system in tin foil boundary conditions, which is the usual case if electrostatics are handled with a Ewald summation technique. See [Neumann1983] for details on the derivation.

Warning

Applying this class requires that no free charges, such as ions or charged fragments, are present in the simulation.

Parameters:

  • atomgroup (MDAnalysis.core.groups.AtomGroup) – Atomgroup on which the analysis is executed

  • temperature (float) – Temperature (Kelvin) at which the system has been simulated

  • make_whole (bool) – Make molecules whole; If the input already contains whole molecules this can be disabled to gain speedup

  • verbose (bool) – Show detailed progress of the calculation

results.M

Directional dependant dipole moment \(\langle \boldsymbol M \rangle\) in \(eÅ\).

Type:

numpy.ndarray

results.M2

Directional dependant squared dipole moment \(\langle \boldsymbol M^2 \rangle\) in \((eÅ)^2\)

Type:

numpy.ndarray

results.fluct

Directional dependant dipole moment fluctuation \(\langle \boldsymbol M^2 \rangle - \langle \boldsymbol M \rangle^2\) in \((eÅ)^2\)

Type:

float

results.eps

Directional dependant static dielectric constant

Type:

numpy.ndarray

results.eps_mean

Static dielectric constant

Type:

float

Example

Create a DielectricConstant instance by supplying an AtomGroup, then use the run() method:

import MDAnalysis as mda
from MDAnalysis.analysis.dielectric import DielectricConstant
from MDAnalysisTests.datafiles import PSF_TRICLINIC, DCD_TRICLINIC

# Load a pure water system
universe = mda.Universe(PSF_TRICLINIC, DCD_TRICLINIC)

diel = DielectricConstant(universe.atoms)
diel.run()
print(diel.results)

The static dielectric constant of the provided atomgroup is saved within the Results attribute.

Added in version 2.1.0.