4.8.4. Dielectric — MDAnalysis.analysis.dielectric

Authors

Mattia Felice Palermo, Philip Loche

Year

2022

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.

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.

New in version 2.1.0.