Lecture 13: The Structure of Classical Fluids

13.1 Recommended textbooks

Chandler Chapter 7.1-7.3

13.2 Topics in this lecture

• Reduced configurational distribution

• Radial distribution function

13.3 Andersen thermostat

We ended the last lecture by discussing the Andersen thermostat for performing MD simulations
that sample the canonical ensemble, but ran out of time just before presenting the algorithm. An
algorithm for a MD simulation using the Andersen thermostat consists of the following steps:

1. Choose a starting configuration, rN (t = 0).

2. Generate initial particle velocities, vN (t = 0), by sampling from the Maxwell-Boltzmann

velocity distribution at a given temperature T .

3. Compute the forces acting on all particles, fN (t).

4. Update the positions to time rN (t + ∆t).

5. Update the velocities to vN (t + 1/2∆t) according to the Velocity-Verlet algorithm.

6. Calculate the new forces fN (t + ∆t).

7. Finish the velocity update to vN (t + ∆t)

8. Iterate over all particles and stochastically attempt to select a particle with probability η∆t;
if selected, reset the particle velocity vector by sampling each component from the Maxwell-
Boltzmann velocity distribution.

9. Repeat steps 3-8 until a sufficient number of timesteps have elapsed. Periodically compute
and save the value of some observables (e.g., temperature, pressure).

10. Approximate the ensemble-average value of the saved observables by averaging over states
sampled during a period of time during which the system is at equilibrium.

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University of Wisconsin-Madison Lecture 13
CBE 710, Fall 2019 - Prof. R. C. Van Lehn October 17, 2019

Note again that this algorithm now introduces a stochastic element to molecular dynamics,
unlike the basic MD algorithm which in principle is deterministic. Finally, it is important to
recognize that the Andersen thermostat is just one simple approach for maintaining the system
temprature, and is no longer commonly used in practice in favor of more advanced techniques (e.g.
the Nose-Hoover thermostat) that are considered more reliable.

13.4 Importance of liquid structure

We have now outlined the algorithms underlying the Monte Carlo and Molecular Dynamics tech-
niques and identified methods for sampling from the canonical ensemble, which is an appropriate
ensemble for many systems. We have emphasized the point that during these simulations it is
important to sample some simulation observable, then by proper averaging at the conclusion of
a simulation we can gain some insight into the behavior of our system. Previous observables we
have discussed included the temperature and energy. In this lecture, we will describe a different
observable that is related to the structure of a set of particles, which will both give important
information about the phase of the system being studied as well as its thermodynamic properties.
Consider a set of particles that we want to classify as being gas-like, liquid-like, or solid-like.
One thing we know about these different phases is that their spatial arrangement of particles is
dramatically different. In a solid, particles tend to be clustered very near to each other in their
crystalline arrangements, while in a gas they tend to spread far apart. A liquid falls somewhere in
between, where particles are condensed but lack the ordered structure inherent to solids. Knowing
this, we can interpret the structure of a liquid by looking at the relative positions of two particles.
That is, if particles tend to be near each other, they are more solid-like; particles that have no
preference for being close to each other are more gas-like. We can quantify this thinking by studying
the radial distribution function as we will now discuss.

13.5 Reduced configurational distribution

First, let us again show that we can ground this discussion in the study of statistical mechanics,
assuming that any given fluid system of interest can be treated as at constant N V T (we could
generalize to N P T without much difficulty). Recall that we can write the canonical partition
function for a classical fluid using the notation:
Z
drN exp −βE(rN )
 
Z= (13.1)
VN

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University of Wisconsin-Madison Lecture 13
CBE 710, Fall 2019 - Prof. R. C. Van Lehn October 17, 2019

This expression integrates over all possible particle configurations in a continuous space with
phase space volume V N , representing all possible combinations of positions. Here, we let E(rN )
refer to only the potential energy of the system associated with particle-particle interactions and
ignore the kinetic energy contribution due to particle velocities, as we have noted previously that
velocities are only a function of the temperature and not particle positions. Alternatively, we can
also write this integral by breaking up rN into each of the N different position vectors for the
different particles.
Z Z Z Z
Z= dr1 dr2 dr3 · · · drN exp [−βE(r1 , r2 , r3 , . . . rN )] (13.2)
V V V V
Here, subscripts indicate the index of one particular particle. Using either notation, the prob-
ability of finding the system in some configuration rN is:

exp −βE(rN )
 
N
p(r ) = R N N
(13.3)
V N dr exp [−βE(r )]
exp [−βE(r1 , r2 , r3 , . . . rN )]
=R R R R (13.4)
V dr1 V dr2 V dr3 · · · V drN exp [−βE(r1 , r2 , r3 , . . . rN )]
This probability distribution function is called the configurational distribution in analogy to the
velocity distribution discussed last class. Again, this is technically a probability density function,
like the Maxwell-Boltzmann distribution, and is the probability of observing the system in a small
volume of phase space near rN ; it has units of volume−N as a result since rN has units of V N .
Now, let’s consider a different question. Rather than asking the probability of a particular
configuration of particles, let’s ask the probability that particle 1 is at position r1 . Recall that back
in our derivation of the canonical ensemble, we divided a combined system into a small system
of interest and a bath, and we said that the probability that the bath obtains a microstate is
proportional to the number of equivalent bath states. We can use the same idea here, and say that
the probability of a configuration in which a specific particle has some particular position is given
by integrating the probability of a system configuration over all other particle positions. In other
words, we can write the following:
R R R
V dr2 V dr3 · · ·
drN exp [−βE(r1 , r2 , r3 , . . . rN )]
V
p(r1 ) = (13.5)
Z Z Z Z
= dr2 dr3 · · · drN p(rN ) (13.6)
V V V
What this expression says is that we fix the position of particle 1 at r1 , then we integrate the
probability density function over the rest of the phase space where the other particle positions
can obtain any value. This expression is referred to as a reduced configurational distribution
because we are now asking the probability of being in one specific region of phase space (i.e., the
region where the position of particle 1 is fixed). This expression assumes that there is a particular
particle with index 1 at position r1 . Alternatively, we could insead calculate the probability that
any of N identical particles is at position r1 as opposed to a specific tagged particle. Since the
particles are identical, this probability is just N times larger, leading to:

p̃(r1 ) = N p(r1 ) (13.7)

Z Z Z
=N dr2 dr3 · · · drN p(rN ) (13.8)
V V V

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University of Wisconsin-Madison Lecture 13
CBE 710, Fall 2019 - Prof. R. C. Van Lehn October 17, 2019

This expression is referred to as a generic reduced configurational distribution, with the

term generic emphasizing that any particle can occupy position r1 . Let’s extend this concept to
multiple positions. Now, we can calculate the probability that any particle is at position r1 and
any particle is at position r2 . Again, we fix these positions, then integrate over the positions of all
other particles. We recognize that there are N ways to choose the first particle and N − 1 ways to
choose the second. Our expression is then:

Z Z
p̃(r1 , r2 ) = N (N − 1) dr3 · · · drN p(rN ) (13.9)
V V

We could continue to generalize this notation, but there is no need for our present purposes.

13.6 The radial distribution function

Let’s consider simplifying these two reduced configurational distribution functions for a system
consisting of a homogeneous, isotropic fluid. That is, assume the fluid is uniform spatially - the
properties of the system are unchanged if I look in any direction through the fluid. Equivalently,
an isotropic fluid can be thought of as one in which translating/rotating all particle positions does
not influence the probability of a configuration; an anisotropic fluid would be one in which such
manipulations would change the system energy (e.g. due to interactions with system boundaries).
First, consider the expression:
Z Z Z
p(r1 ) = dr2 dr3 · · · drN p(rN ) (13.10)
V V V
This expression is the probability density function for finding a particle in some small vol-
ume, dV , centered at some position r1 . Since the particle has to be within the volume, then the
probability density function is normalized such that:
Z
p(r1 )dr1 = 1 (13.11)
V
That is, the probability when summed over all possiblve values of r1 within the volume has to be
one. For an isotropic fluid, there will be an equal likelihood that we can find a single particle at
any position in the volume since we are integrating over the positions of all other particles - there
is no reason why any one position should be favored over another. Therefore, the normalization
condition enforces that p(r1 ) = 1/V , indicating an equal likelihood of finding a particular particle
anywhere in the volume. The generic reduced configurational distribution for a single particle is
then:

N
p̃(r1 ) = N p(r1 ) =≡ρ (13.12)
V
Here, ρ is simply the number density of the system. Thus, the density of the system tells us
the probability of finding a particle in any given small volume of the system independent of the
positions of its neighbors.
Now let’s consider the reduced configurational distribution for two particles:

Z Z
p̃(r1 , r2 ) = N (N − 1) dr3 · · · drN p(rN ) (13.13)
V V

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University of Wisconsin-Madison Lecture 13
CBE 710, Fall 2019 - Prof. R. C. Van Lehn October 17, 2019

Unlike the former case of studying only a single particle, now there are possible correlations
between particles. That is, certain pairs of positions may be more likely than others due to the
interaction of particle 1 and 2, even when integrating over the positions of all other particles.
Let’s first assume that the particles in our system are completely uncorrelated because they do not
interact; that is, we have an ideal gas. In that case, the probability p(r1 , r2 ) can be factorized into
two single-particle probability distributions since the two particles are independent of each other.
We can then write:

Z Z
p̃(r1 , r2 ) = N (N − 1) dr3 · · · drN p(rN ) (13.14)
V V
= N (N − 1)p(r1 , r2 ) (13.15)
= N (N − 1)p(r1 )p(r2 ) if positions are independent/uncorrelated (13.16)
N (N − 1)
= (13.17)
V2
2
≈ρ (13.18)

Here, we assume that N  1 for a typical system and approximate this joint probability
distribution function as the density squared. This result is true for an ideal gas, but in general a
real system will have some deviation from ideality that emerges from interactions between pairs of
particles. We will define a function, g(r1 , r2 ), as:

p̃(r1 , r2 )
g(r1 , r2 ) = (13.19)
p̃(r1 , r2 )ideal
p̃(r1 , r2 )
= (13.20)
ρ2
This expression is called the pair-correlation function because it reflects the tendency for
pairs of particles to be distributed at certain positions relative to each other with probabilities that
deviate from what would be expected for an ideal gas. The expression would be 1 for all pairs of
positions for an ideal gas. For completeness we can rewrite this as:

dr3 · · · V drN p(rN )

RR
N (N − 1) V
g(r1 , r2 ) = (13.21)
ρ2
N (N − 1) V dr3 · · · V drN exp −βE(rN )
R R  
= (13.22)
ρ2 Z

This expression will be useful in the next lecture. For an isotropic system, g(r1 , r2 ) only depends
on the distance between two particles, r = |r1 − r2 |. Again, this is because all directions in an
isotropic fluid are equivalent, so if we rotate the entire system there is no change in the probability.
Equivalently, I can imagine placing particle 1 at some position, then placing particle 2 a distance r
away - rotating the entire system, including particle 2, while preserving the same distance r does
not change the system properties. For an isotropic system we can then write the pair-correlation
function as:

g(r) ≡ g(r1 , r2 ) (13.23)

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University of Wisconsin-Madison Lecture 13
CBE 710, Fall 2019 - Prof. R. C. Van Lehn October 17, 2019

where r is the scalar distance between particles at position r1 and r2 . g(r) is called the radial
distribution function.
If we assume that one of these particles is always at the origin of the coordinate system, and we
know that the probability of that particle being at the origin is ρ since that is the single-particle
reduced distribution function, then we arrive at the result:

p̃(r1 , r2 )
g(r1 , r2 ) = g(r) = (13.24)
ρ2
p̃(r1 = 0)p̃(r1 = 0, r)
= (13.25)
ρ2
p̃(r1 = 0, r)
∴ g(r) = (13.26)
ρ
Here, we write the conditional probability density that any particle is at a distance r away from
any particle placed at the origin. Hence we finally achieve the following definition: for a given
particle i in a system, which we will say is “tagged” and placed at the origin of the coordinate
system, the radial distribution function tells us the probability of a particle being a distance r away
from the tagged particle relative to what would be observed in an ideal gas. Alternatively, we could
say that the quantity ρg(r) tells us the average number density of particles at a distance r away
from a single tagged particle. This last definition is probably the most intuitive.

13.7 g(r) for different states of matter

Having defined g(r), let’s qualitatively discuss how it should behave. As we said, for an ideal gas,
the radial distribution function should be exactly 1 for all distances r between a tagged particle
and any other given particle on average. For a real gas, then, the average density will approach the
overall density at far distances, but g(r) will be zero for distances less than the diameter of each gas
particle - that is, real gases exclude volume. There is also like some enhanced average density at
close distances between particles, reflecting some weak attractive intermolecular interactions. For
solids, in which atoms are in very precise spatial positions, g(r) will have sharp peaks reflecting
the typical distances between atoms in crystalline materials. Finally, for liquids, g(r) will fluctuate
around the bulk density, with high density regions reflecting so-called solvation shells where atoms
prefer to accumulate due to favorable interactions. Thus, calculating g(r) alone can tell us structural
information, such as the preferred distances between particles. Moreover, we can derive a series of
other thermodynamic properties from this expression, one of which will be discussed below. First,
however, let us discuss how to calculate this quantity in a simulation.

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University of Wisconsin-Madison Lecture 13
CBE 710, Fall 2019 - Prof. R. C. Van Lehn October 17, 2019

13.8 Calculating g(r)

Let’s now talk about how to algorithmically calculate g(r) based on our above discussion. In
principle, g(r) is a continuous quantity, but in a MD simulation we discretize space. Therefore, we
can calculate g(r) by populating a histogram of pairwise distances and normalizing appropriately.
We divide the distance, r, into a set of bins of width dr that discretizes the distance coordinate.
We can number the bins such that bin i refers to the set of distances between dr × i and dr × (i + 1).
Each bin then refers to a volume of space given by 4π 3 3 3
3 dr [(i + 1) − (i )].
Recalling that our definition of g(r) is the average density of particles a given distance r apart
divided by the overall density, we can write the following algorithm:

1. During a converged simulation, periodically iterate over all particles. For each particle, cal-
culate the distance r to every other particle.

2. For each distance, calculate the corresponding index of the bin in the histogram; that is,
calculate r/dr and round to an integer (or round down, depending on how you define your
bins). Increase the value of this bin by 1.

3. Repeat steps 1 and 2 a number of times during a simulation (i.e., every time you save the
energy after convergence).

4. Normalize the histogram at the end of the simulation. This requires dividing each bin by the
number of samples (to time average), the number of particles in the system (since we iterate
over all particles each timestep), and the volume of the bin (to get a density). Finally, divide
all bins by the bulk density (N/V ) to get g(r).

Symbolically, this procedure can be written as:

*N N +
1 1 1 XX
g(r) = δ(r − rij ) (13.27)
ρ N V (r)
i j6=i

The function δ(r − rij ) is a delta function that returns 1 if the distance is within the small
binwidth of dr around the desired distance r; this is captured by incrementing bins in our histogram.
The ensemble-average of this sum is equal to averaging over the number of samples (i.e., time-
averaging). The term 1/V (r) normalizes each bin by its volume to get an average density per bin.
The term 1/N normalizes the sum by the number of particles, since we iterate over all particles
each time we sample. Finally, 1/ρ normalizes g(r) by the bulk density as desired. Calculating this
for each value of r would yield a complete g(r) curve.