Measurement Science and Technology

Meas. Sci. Technol. 28 (2017) 014003 (7pp) doi:10.1088/1361-6501/28/1/014003

Can molecular dynamics help in

understanding dielectric phenomena?
Roberto Olmi1 and Marco Bittelli1,2
1
  Institute of Applied Physics, National Research Council Via Madonna del Piano, 10, 50019 Sesto
Fiorentino (Firenze), Italy
2
  Department of Agricultural Science, University of Bologna Viale Fanin, 44, 40127 Bologna, Italy

E-mail: r.olmi@ifac.cnr.it and marco.bittelli@unibo.it

Received 29 June 2016, revised 28 October 2016

Accepted for publication 1 November 2016
Published 25 November 2016

Abstract
Molecular dynamics (MD) is a modeling technique widely used in material science as well as
in chemical physics, biochemistry and biophysics. MD is based on ‘first principles’, allowing
one to compute the physical characteristics of a material, such as density, heat capacity,
isothermal compressibility and also the dielectric constant and relaxation, mixing a classical
physics approach and statistical mechanics. Although a number of papers exist in the literature
concerning the study of the dielectric properties of liquid and solid materials, the MD
approach appears to be almost ignored in the electromagnetic aquametry community. We use a
rather simple example, a mixture of ethanol and water at various concentrations, to introduce
MD as a theoretical tool for investigating the dielectric behavior of more complex moist
substances. We show that MD simulations suggest a time-domain model for alcohol–water
solutions, consisting in a mixture of a KWW stretched-exponential and a simple exponential,
whose validity could be subjected to an experimental verification.

Keywords: molecular dynamics, molecular modeling, dielectrics

(Some figures may appear in colour only in the online journal)

1. Introduction the University of Groeningen in 1991 and is nowadays very

Theoretical models and measurement science are tightly
bound. The ‘plain’ measurement process involves a measuring
instrument, an object to be measured and an environment. But
the real purpose of measurements is the confirmation or the
rejection of a model of the real world. In such a context, simu-
lation methods based on ‘first principles’, i.e. subordinated
to the weakest possible physical constraints, play an impor-
tant role in the interpretation of the measurement results. The
experimental study of the physical properties of molecular
systems (e.g. the dielectric properties) can benefit from the
application of broad class of computer-simulation techniques
known as ‘molecular modeling’.
Among those techniques, molecular dynamics (MD) was
first introduced in the late 50s [1], but the application to large-
scale problems had to wait for the explosive improvement
of the computational power in the last 20 years. Indeed, the
GROMACS (GROningen MAchine for Chemical Simulations)
package [2], that we used in this paper, was first released by
widely employed as it is totally free and it runs faster than
many other MD simulation programs.
The idea behind MD is that of computing how a system of
particles (atoms, molecules, coarse-grained structures) evolves
under the laws of classical mechanics. Although a rigorous
solution of a many-body problem at the atomic level would
require quantum mechanics, a semi-empirical approach can be
used that is based on classical mechanics and statistical physics.
Every particle is assigned a proper potential function (usually
called a Force Field in the MD community) that is used to
compute the interactions among particles as a function of their
coordinates. Force Fields usually subdivide the potential func-
tions in two broad classes: bonded interactions, describing the
forces among atoms in a molecule (more precisely, describing
the interaction of up to four atoms, i.e. of a dihedral), and non-
bonded interactions between atoms in different molecules.
The former consist in potential terms due to bond stretching,
to the bending of bond angles and to the torsion due to the
rotation around bonds. The latter include short-range, van der

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Meas. Sci. Technol. 28 (2017) 014003
Waals interactions, and long-range, electrostatic ones. van der
Waals pair interactions are usually modeled by the empirical
Lennard-Jones function describing a ‘potential well’:
⎡⎛ δ ⎞12 ⎛ δ ⎞6⎤
VLJ(r ) = 4α ⎢⎜ ⎟ − ⎜ ⎟ ⎥
⎣⎝ r ⎠ ⎝r ⎠ ⎦
(1)
for a spherical particle of diameter δ, where α is the depth of
the potential well.
Practically, an MD simulation consists in solving the
Hamiltonian’s equations of motion or, in other terms in inte-
grating the Newton’s equations for each particle:
→ ∂V (r→1, …, r→N )
Fi = −
∂r→i
∂ 2r→i → the motion of the fastest particles. When hydrogen atoms are
mi = Fi
∂t 2
where the total potential V is a sum of terms such as:
V (r ) = VB(r ) + VNB(r ) = (Vbonds + Vangles + Vtorsion )B
 computations over infinite distances, when long range interac-
+ (VLJ + Vcoulomb )NB (2)
The shape of the different terms in (2) is described in all MD
texts, for example in the introductory paper [3], and it is briefly
summarized in the following. Bond stretching and bond angle
potentials are usually assumed as harmonic:
1 MD simulations are performed at constant temperature,
Vbonds =
2
∑ kij (rij − req )2
bonds
1 mechanics), or in a NPT (number, pressure, temperature)
Vangles =
2
∑ hijk (θijk − θeq )2
bond angles
respectively involving pairs and triads of atoms. The torsion
potential depends on a torsion angle φ, and it is generally
described as a cosine expansion:
1 ergodic hypothesis, one of the most fundamental axioms of sta-
Vtorsion =
2
∑ An [1 + cos(nφ − γ )]
torsion angles
An and γ being constant depending on the molecule geometry.
The pair correlation potential represents the ‘essential’ physics,
but it is clearly a simplification as an n-body problem would
require also higher-order terms. Such an approx­imation, how-
ever, has been demonstrated to be sufficient [4] for describing
the physical properties of real liquids if the average three-body
effects are included in an effective pair potential.
A thorough discussion of the huge number of different
Force Fields used in the literature is beyond the scope of this
paper. Potentials used for large molecules in condensed phase
include AMBER (assisted model building with energy refine-
ment) [5], CHARMM (chemistry at Harvard macromolecular
mechanics) [6], OPLS (optimized potentials for liquid simu-
lations) [7] and many others. The functional form of all those
potentials is described by the above three interaction terms,
while their specific parametres are typically determined by
quantum chemical computations and by experimental data.
The last non-bonded interaction term is the straightforward
Coulomb potential between the charges qi and qj a distance
rij apart:
2
R Olmi and M Bittelli
qiqj
Vcoulomb = ∑
i, j 4πε0rij
The equations  of motion are numerically solved at discrete
time steps, using various integrators like the Verlet and the
leap-frog algorithms [3]. Given the coordinates of an initial
‘meaningful’ geometric configuration of particles, and given
their velocity distribution, the position and velocity of each
particle is computed at every time step as a consequence of the
potentials (i.e. of the force) on each atom. In other words, the
particle system is evolved in time, updating the coordinates at
every time step. The choice of the time step is critically impor-
tant, in particular it should be as large as possible to reduce
the computation time (most of which is spent in computing
forces) but it must be small enough to properly reproduce
involved, the time step is as low as 1–2 fs.
To simulate an infinite medium, at least in the directions
in which the interaction with the container is not of interest,
periodic boundary conditions are applied. In order to avoid
tions are involved, several techniques are employed for poten-
tial truncation: from cut-off approaches, involving an abrupt
decay of the interaction (working well on LJ short range inter-
actions, but not on Coulomb ones), to techniques manipulating
the interactions by splitting them into slow and fast parts, as
the particle–mesh Ewald (PME) summation method [8].
in a so-called NVT (number of particles, volume, temper­
ature) ensemble (known as canonical ensemble in statistical
ensemble, i.e. in isothermal conditions at constant volume or
pressure. Statistical mechanics come into play when, in order
to estimate a physical property (in our case, the dielectric con-
stant), an average is performed on the computed geometrical
configurations. The key point in the average calculation is the
tistical physics stating that the ‘ensemble’ average of a quantity
A can be computed as the ‘time’ average of the same quantity:
A ensemble = A time
meaning that during the time evolution the system will even-
tually pass through all possible states. The temperature and
pressure control are accomplished by means of a numerical
thermostat and barostat, respectively. In practice, temperature
is controlled by rescaling the particle velocities, while pres­
sure requires rescaling the coordinates at each time step. The
above described thermostat clearly violates energy conserva-
tion, therefore it must be used only as a control step, i.e. data
must not be collected at this stage. After bringing a system to
a desired state (for example at a given temperature) it must be
left free to evolve without such kind of constraints.
As stated at the beginning, MD is an approximate method.
In particular, it does not take into account electrons, as
quantum effects are not modeled, and as such MD is not able
at all in simulating the creation of rupture of chemical bonds
and, in principle, it could not be used for rigorously inves-
tigating hydrogen bonds (that have a quantum mechanical
nature). However, investigations of H-bond distributions are
Meas. Sci. Technol. 28 (2017) 014003
often found in the literature, based on the ‘crude’ approx­
imation of describing them as Coulomb interactions of atomic
point charges. As a frequently cited primer on MD points out
[9], ‘the realism of the simulation depends on the ability of
the potential chosen to reproduce the behavior of the material
under the conditions at which the simulation is run’.
2.  Simulation of ethanol–water mixtures
The interest in ethanol–water mixtures is motivated by the
wide use of ethanol in industrial processes and because the
most part of alcoholic beverages are based on such solutions.
Apart from that, alcohol/water mixtures are interesting in
themselves, because they can constitute a simple model for
studying the hydrophobic effect. Indeed, alcohols have an
amphiphilic character, i.e. they possess both hydrophobic and
hydrophilic parts.
From a scientific point of view, alcohols have been studied
for a long time, with various analytical methods and for dif-
ferent objectives. The dielectric relaxation properties of pure
alcohols and in water solutions are still an actual research
topic, particularly in relation with hydrogen bonding and the
fluctuation of hydrogen networks [10, 11]. MD simulations
have been conducted related to the study of alcohol hydration
[12] and specifically on the analysis of hydrogen-bonded pairs
[13].
The dynamic properties of ethanol–water mixtures have
been numerically investigated for the purpose of studying
the relation between mobility and viscosity [14]. Dielectric
properties of pure ethanol have been studied by means of MD
[15]. In this paper, the dielectric relaxation of ethanol–water
mixtures are investigated by MD as a function of the ethanol
mass fraction.
2.1.  GROMACS implementation
The MD simulations have been conducted using GROMACS
[16, 32], version 5.0.7, employing two force fields: the
simple point charge (SPC/E) [17] for the water molecules,
and the all-atoms optimized potential for liquid simulations
(OPLS-AA) [18] for ethanol. Needless to say, several other
force fields have been developed, for example the largely used
TIP3P potential whose characteristics are compared to SPC/E
in [19].
The size of the simulation box and the number of ethanol
and water molecules, respectively NE and NW, have been
computed such to give the correct mass fraction of ethanol in
water, i.e. in terms of the molar masses of ethanol and water:
MENE
c ETH(%) =
(3) × 100
MENE + MWNW
GROMACS is a command line code running under Linux.
A number of scripts have been developed to perform the fol-
lowing steps:
1. Energy minimization. The initial configuration, con-
sisting in NE molecules of ethanol and NW molecules of
water is a random one, not respecting the intermolecular
3
R Olmi and M Bittelli
Table 1.  Number of ethanol and water molecules.
cETH (%) NE NW
0 0 216
20 100 1022
40 100 383
60 100 170
80 100 64
100 216 0
distances in a liquid mixture. In this step, the system
is evolved assuming flexible bonds, treating long range
interactions by the PME summation method. Integration
of the equations  of motion is performed by a steepest
descent algorithm, with 10 fs step size, for a total time
duration of 500 ps. The suitability of the final configura-
tion is tested by looking at the behavior of the system
potential energy, that should converge to a negative
value.
2. Equilibration. Once a reasonable geometry has been
obtained, solute and solvent should be equilibrated at
constant temperature (NVT ensemble) and at constant
pressure (NPT ensemble). For that purpose, 100 ps of
NVT simulation at 300 K are followed by 100 ps of NPT
simulation at 300 K and 1 Atm, with PME long range
electrostatics and reducing the time step to 2 fs. In both
cases, the molecules are taken rigid (i.e. not flexible)
using LINCS bond constraints, to reduce the computa-
tional time. Integration is performed using the leap-frog
algorithm. At the end of the first half-step (isothermal run)
the constancy of temperature during time is checked as a
control variable. After the isobaric step, the constancy of
pressure is checked, and the density of the alcohol–water
mixture can also be computed.
3. Production. The physical quantities of interest are com-
puted during the last step. As in step 2, a time step of
2 fs is used, again with leap-frog integration. This time,
however, the system must evolve for a time sufficiently
long to allow the relevant physics to reach steady state
conditions. A total time od 20 ns is chosen, also on the
basis of the considerations reported in [20] concerning
the minimum time required for dielectric simulations.
For the case of pure ethanol, the total simulation time has
been increased to 40 ns, in consideration of the expected
greater relaxation time.
Table 1 summarizes the number of molecules used in the
MD unit cell. The simulations employed a cutoff of 0.9 nm for
Lennard-Jones interactions. All simulations refer to a temper­
ature of 300 K and a pressure of 1 Atm.
The proper number of ethanol molecules is inserted in a
cubic box, by means of specific GROMACS commands. The
size of the box is chosen such to contain the total number of
molecules, with reference to table 1. For example, referring to
the second row (0.2 ethanol mass fraction) the box is gener-
ated by means of:
gmx insert-molecules -ci 1-ethanol.pdb -nmol 100 -o ethanol.
pdb -box 3.5 3.5 3.5
Meas. Sci. Technol. 28 (2017) 014003
using the geometry (ethanol.pdb) of a single ethanol mole-
cule. In the above case, the initial cubic box side is 3.5 nm.
The choice of a small number of molecules in the MD cell
is assumed to do not significantly alter the physical ‘picture’.
Indeed, simulations with an increasing number of molecules
in the case of pure water show a moderate influence on the
relaxation dynamics (as briefly discussed in section 3.1).
2.2.  Dielectric relaxation model
It is well known that the static dielectric constant of a polar
liquid can be computed from the fluctuations of the total dipole
moment [21]. A thorough analysis of the computer simulation
of polar systems has been developed in [22]. Although flexible
(polarizable) models are available for computing the dielectric
properties of polar liquids, here a rigid molecular model is
adopted, which greatly reduces the computational time and
has been proved to give meaningful results. The rigid model
assumes a limit high-frequency permittivity equal to 1, and
the low-frequency value is given by:
M2 − M 2
εs = 1 +
(4)
3ε0VkBT
where M is the total dipole moment, 〈M2〉 and 〈M〉2 are
averages of the squared M and the square of the average
M, ε0 is the permittivity of vacuum, V the volume of the
MD cell, kB the Boltzmann constant and T the temperature.
Equation (4) assumes a periodic arrangement of molecules,
i.e. the simulation volume is infinitely repeated in all the
spatial directions.
The relaxation dynamics depends on the auto-correlation
function (ACF) of the total dipole moment M. Effectively, the
frequency-dependent electric permittivity is expressed as the
Laplace transform of the pulse-response function [23].
ε (ω ) − 1 ⎡ dφ ⎤
= L ⎢− ⎥ = 1 − L [ φ ]
⎣ dt ⎦
(5)
εs − 1
In the linear response approximation [24], the thermal fluc-
tuations of the polarization are equivalent to the macroscopic
re-alignment caused by an external electric field, therefore the
relaxation function coincides with the dipole ACF:
→ →
M (t ) ⋅ M (0)
φ (t ) =
(6) → 2
M (0)
and the frequency dependent permittivity is obtained [25]
combining equations (4)–(6).
GROMACS allows computing the static dielectric constant
εs of a system of molecules, by using the equivalence among
time averages and ensemble averages or, in other words,
assuming the ergodic hypothesis as true. The code also allows
to obtain the normalized ACF Φ of the system, using the time-
domain results obtained during the production phase (see sec-
tion 2.1). Once the above characteristics have been computed,
the permittivity is obtained by a Laplace (or Fourier) trans-
form of the time-derivative of the ACF or, in practice, of a
function ϕ fitting it:
4
R Olmi and M Bittelli
Figure 1.  Density versus ethanol mass fraction: comparison among
real-solution data (black line with markers) and average densities
computed by MD (red line).
⎡ ⎛ ⎡ dϕ ⎤⎞⎤
ε′(ω ) = C ⎢1 +(εs − 1)R⎜L ⎢− ⎥⎟⎥
⎣ ⎝ ⎣ dt ⎦⎠⎦

⎛ ⎡ dϕ ⎤⎞
ε″(ω ) = −C (εs − 1)I⎜L ⎢− ⎥⎟ (7)
⎝ ⎣ dt ⎦⎠
where the constant C is such to give a low-frequency limit
value equal to εs.
3. Results
Six molecular assemblies have been considered, corresponding
to the ethanol mass concentrations reported in table 1. At the
end of the simulations, various physical characteristics can be
computed in addition to the dielectric properties. In particular,
as the dielectric constant is somehow related to the density,
this last parameter has been calculated and compared to the
expected value for a real ethanol–water mixture. Figure  1
compares the MD-densities with the values taken from the
literature [26].
The excellent agreement between computed and true den-
sity makes us confident about the correctness of the simula-
tion, together with other control parameters not shown here
(e.g. the total potential energy of the system, the average
temper­ature and pressure).
The dielectric properties and the relaxation dynamics of
ethanol–water mixtures have been thoroughly studied starting
from experimental data. Usually, in the frequency domain a
mixture of relaxation functions is adopted to represent the
behavior of the alcoholic solution [27]. The asymmetric shape
of the dielectric losses suggests that the dielectric function in
the time domain can consist in a stretched exponential, also
known as Kohlrausch–Williams–Watts (KWW) function [28],
or in a sum of such a function and a simple exponential, as we
propose here for the ACF. Indeed, the relation among the time-
domain KWW function and the frequency-domain Havriliak–
Negami (HN) distribution has been established [29], although
Meas. Sci. Technol. 28 (2017) 014003
Figure 2.  The normalized ACF for an ethanol–water mixture with
40% ethanol: (a) computed ACF (cross symbols) compared to
simple exponential fitting (dashed line) and exponential mixture (8)
(solid line); (b) log(ACF) versus time in the first 60 ps.
a closed-form expression is not available. Therefore, a sum of
a KWW, bringing to a HN in the frequency domain and thus
well representing the ethanol relaxation, and a simple expo-
nential, representing water relaxation, appears very reason-
able. As it is well known, the Debye relaxation is the Laplace
transform of an exponential function. Equation (8) shows such
a fitting function.
⎡⎛ t ⎞ α ⎤ ⎛ t ⎞
φ(t ) = AKWW exp ⎢⎜ ⎟ ⎥ + AD exp⎜ ⎟
⎣⎝ τKWW ⎠ ⎦ ⎝ τD ⎠
(8)
Figure 2(a) shows, as an example, the ACF obtained by the
MD computation for an ethanol mass fraction of 0.4 (cross
symbols). Superimposed, the best fitting obtained with a
simple exponential (red dashed line) and with function (8)
(blue solid line). It is clear that a single exponential is not
able to accurately represent the relaxation dynamics in the
first 100 ps. At times greater than 200 ps the computed ACF
fluctuates around zero, making the choice of the fitting func-
tion quite arbitrary in that time region.
Figure 3 shows the relaxation times obtained on all mat­
erials. It compares the KWW relaxation times (the Debye
terms are not reported there) for pure ethanol and for solutions
at decreasing ethanol fraction, with the Debye relaxation time
computed for pure water.
5
R Olmi and M Bittelli
Figure 3.  The computed relaxation times as a function of the
ethanol mass fraction (see text).
Figure 4 shows the dielectric spectra (real and imaginary
part) of the analyzed molecular systems. The computation of
the spectrum requires to compute the Laplace transform (actu-
ally, the FFT (fast Fourier transform) is computed instead) of
the ACF, using (7). The plots concerning the dielectric con-
stant (on the left) refer to an ethanol concentration increasing
from 0 (pure water) to 100% (pure ethanol). All dielectric
constants are slightly underestimated. This is a well known
situation with rigid-molecule assemblies, but here is not of
great concern, if the aim is that of understanding if MD is
potentially useful for studying water in dielectric models. The
dielectric losses behavior with frequency and ethanol mass
fraction (plots on the right of figure 3) is also rather encour-
aging, correctly showing the expected shift to the right of the
loss maximum with decreasing ethanol.
3.1.  Relevant statistical functions
The radial distribution function (RDF) for oxygen–oxygen
pairs has been computed in the two extreme cases (pure sol-
vents), for comparing the numerical results with experimental
data. The RDF is a statistical function describing the structure
of a substance (actually, describing how the density depends
on the distance from a reference particle) that can be exper­
imentally determined by x-ray or Neutron diffraction methods.
Figure 5 shows the RDF (denoted by gOO) for pure water
(left) and pure ethanol (right), computed for three different
number of molecules (see figure caption). The experimental
RDF for O–O pairs has been reported in [30] for water at
ambient temperature, and for ethanol [31] at 298 K. The
agreement among the computed RDF’s and the experimental
data is very good. The gOO of water experimentally exhibits a
first peak at about 0.34 nm, followed by two smaller maxima
between 0.4 and 0.5 nm and at about 0.7 nm, exactly as the
computed RDF shows. The experimental gOO of ethanol at
298 K has a sharp maximum at about 0.2 nm, as found by
the MD computation, followed by a small peak between
0.3 and 0.4 nm. The dpendence on the size of the MD cell
Meas. Sci. Technol. 28 (2017) 014003 R Olmi and M Bittelli

Figure 4.  Dielectric constant (left) and dielectric losses (right) of the ethanol–water mixtures (see text).

Figure 5.  The RDF of the O–O pairs for pure water (left) and pure ethanol (right) as a function of the number N of molecules.
Symbols:  +  refers to N  =  216, o to N  =  502, X to N  =  1050, solid line to N  =  2258.

Figure 6.  The ACF of pure water (left) and pure ethanol (right) as a function of the number N of molecules. Dotted lines correspond to
N  =  216, dashed line to N  =  502, dash-dot to N  =  1050, solid line to N  =  2258.

is clearly negligible, as the RDF’s of both water and ethanol
do not change when the number of molecules increases of an
order of magnitude, from 216 to 2258 (and the initial box size
increases from 1.8 to 4.1 nm for water, and from 2.9 to 7 nm
for ethanol).
Figure 6 shows the dependence of the normalized ACF of
pure water (left) and pure ethanol (right) from the box size.
At least for the limited range of molecule numbers investi-
gated (respectively, 216, 502, 1050 and 2258 as specified in
the figure caption), the dependence of the ACF on the cell size
is rather moderate, therefore the dielectric relaxation proper-
ties of the smaller model are meaningful.
4. Conclusions
MD simulations, also employing small-size systems, show sev-
eral interesting features of ethanol–water mixtures. In particular,
they suggest that the relaxation dynamics of such materials in the
time domain can be described by a mixture involving a stretched
exponential (or KWW function) and a simple exponential decay,

6
Meas. Sci. Technol. 28 (2017) 014003
that is strictly related to a mixture of a Debye function and of an
HN distribution in the frequency domain.
The results obtained on ethanol–water solutions demon-
strate that MD could contribute to the understanding of the
dielectric behavior of complex moist substances. For example,
it could hopefully provide hints to advance in the comprehen-
sion of the controversial problem of the water bound to a
porous surface.
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