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This is followed by Section IV, where the natural idea that the classical Hamiltonian H(q, p) = K(p) +U(q) with kinetic
long range force calculations dictate asymptotic behaviour is energy K(p) = |p|2 /2 (where the usual factor of mass is unity
extended from the 1D model to many-body systems of arbi- under reduced units) and a general potential U(q). The statis-
trary size in three spatial dimensions. These systems exhibit tical average of a quantity X for this N-body system is given
the physical properties of standard MD simulations: i.e cu- by
bic geometry with periodic boundary conditions that employ
1
ZZ
the minimum image convention. In this way, we perform cal- hXi = X exp[−β H(q, p)] d3 q d3 p , (6)
culations on a principal computational cubic cell of a theo- ZN h3N N!
Ωq ×Ωp
retically infinite simple fluid. In Section IV B, MD results are
displayed for many-body systems. We present the dependence where the Boltzmann factor acts as a statistical weighting for
of the standardised force moments on density, n, and temper- a configuration {q, p} ∈ R6N , normalised such that h1i = 1.
ature, T , and discuss the parameters and integrator schemes We label atoms so that the first one is the tagged atom. De-
utilised in producing the results of MD simulations. noting the force on the tagged atom produced from the j-th
atom by F j = [Fj,1 , Fj,2 , Fj,3 ] ∈ R3 , for j = 2, 3, . . . , N, the to-
tal force F = [F1 , F2 , F3 ] on the tagged atom is
II. NOTATION
N
We consider a system of N identical atoms interacting via the F= ∑ F j.
Lennard-Jones 12-6 potential19 . This is a ubiquitous inter- j=2
We now go on to illustrate three approaches to obtain the de- To further analyze integrals (10), we introduce a cutoff c,
pendence of the force distribution on parameters n and T . It which satisfies that r∗ < c < L/2, where r∗ = 21/6 is a unique
is useful to note that, as we are now working in one spatial maximum of exp[−β U(z)], which can be Taylor expanded as
dimension, density n is proportional to 1/L, i.e. we have β (1 + 4z−6 + 4z−12 − 16/3z−18 + 8z−24 . . . ). Considering suf-
n ∝ 1/L. We will consider a simple system in one spatial ficiently large L, we can choose the cutoff c, so that
dimension consisting of two atoms interacting through the
Lennard-Jones potential (3) in interval [0, L] with periodic
Zc ZL/2
4
f0 (L) − 2 exp[−β U(r)] dr + β 1 + dr ≤ ε , (13)
boundary conditions. One of the atoms is considered to be r 6
fixed at position q0 = L/2 ∈ [0, L] and the other atom is free 0 c
to move, therefore, we have N = 1 free atom. Its position
where tolerance ε is chosen to be 10−4 in our illustrative com-
is denoted x ∈ [0, L]. Therefore, the inter-atomic distance is
putations. This splitting allows us to numerically calculate the
r = |x − q0 |. Using our simplified one-dimensional set up,
bulk of the integral (10) as a constant independent of L and
F1 = F and Ωq = (0, L), equation (7) reduces to
then use the second term to give an analytic expression for αk
ZL with dependence on L, and ultimately on n.
fk (L) = F k (|x − q0 |) exp[−β U(|x − q0 |)] dx, (9) The range of values of T that are of typical use are chosen in
0
order to maintain the liquid state of Argon during simulation.
These are approximately temperatures in the interval 0.70 <
which is the marginalised expected value of the k-th moment T < 0.73 under ambient conditions26 . Therefore, as volume
of force F(x) = −dU/dx, where we have dropped subscripts is varied we are in a regime where β = o(1), for convenience
in the Lennard-Jones potential (3) and we write it as U(z) = we set β = 1. Though given that the density of our system
4(z−12 − z−6 ). Utilising the symmetry of the potential (and changes between each simulation some systems will be in a
therefore the force) we are left with liquid phase and others in a gaseous phase, this is a point of
ZL/2 discussion in Section IV B.
fk (L) = 2 F k (r) exp[−β U(r)] dr. (10) Splitting the integration domain [0, L/2] of integral (10)
into [0, c] and [c, L/2], we use the exact form of the integrand
0
in [0, c] to obtain a ‘near-field’ contribution. Utilising an ap-
In what follows, we will assume that we are in a regime where proximate form for the integrand given by the truncated Taylor
the box width L satisfies L ≫ r∗ , where r∗ = 21/6 minimizes expansion f (z) in the domain [c, L/2] gives rise to a density
the Lennard-Jones potential U. dependent ‘far-field’ contribution. Combining these we arrive
at the approximate form for f0 (L). Using cutoff c = 2, equa-
tion (13) is satisfied with ε = 10−4 . Therefore, upon numer-
A. Differential equation for standardised moments ically calculating the bulk contribution for the integral with
domain [0, 2], we get
We consider a perturbation of the form L → L + δ L. Using
equation (10) and considering terms to the order O(δ L), we ZL/2
obtain f0 (L) = 2 exp[−β U(r)] dr = b0 + L + o L−6 (14)
0
fk (L + δ L) = fk (L) + fk′ (L) δ L + o δ L2
with b0 = −0.71832, which depends on our choice of cut-
= fk (L) + F k (L/2) exp[−β U(L/2)] δ L + o δ L2 .
off c = 2. Similarly, we can calculate far-field integral ap-
Using equation (8), we approximate αk (L + δ L) by proximations of integrals (10) for general values of k =
2, 4, 6, 8, 10, 12. The integrand F k (r) exp[−β U(r)] has max-
αk (L) + αk (L) υk (L) exp[−β U(L/2)] δ L + o δ L2 ,
ima when r = r∗ = 21/6 or when kU ′′ (r) = β (U ′ (r))2 . This
where our notation αk (L) highlights the dependence of the forms a cubic in r6 that can be solved. For the values of k
standardised moments of force, αk , on L, and function υk (L) used in this work, this sometimes results in a global maxi-
is given by mum, that always lies at a distance less than r < r∗ from the
origin. Therefore r∗ = 21/6 is the furthest maximum of the
k−2 F k (L/2) k F 2 (L/2) integrand from the origin.
υk (L) = + − . (11)
2 f0 (L) fk (L) 2 f2 (L) Splitting integral (10) into a near-field and far-field contri-
Taking the limit δ L → 0, we obtain the derivative of the k-th bution, using the general cutoff c = 2, we find
standardised moment of force, with respect to L, as
fk (L) = bk + o L−7k (15)
∂ αk
(L) = υk (L) exp[−β U(L/2)] αk (L), (12) The near-field contributions, bk , generally increase vastly if
∂L
we increase the value of k, for example
where υk (L) are expressed in terms of integrals (10) as given
by equation (11). b0 = −0.71832, b2 = 130.64 and b4 = 2.5727 × 105 , (16)
On standardised moments of force distribution in simple liquids 4
Since L/2 > r∗ , the force F(L/2) monotonically decreases as D. Temperature dependence of standardised moments
a function of L. When looking at leading order approxima-
tions in the low density limit n → 0 (equivalent to limit L → ∞) One can perform a similar analysis as in Section III A, viewing
to equation (12), we need to analyse υk (L). The second and the moments αk = αk (T ) as a function of temperature T =
third term in equation (11) converge to zero more rapidly than 1/β . To do that, we consider the moment definition (10) as a
the first term as L → ∞, therefore the leading order behaviour function of temperature T , namely, we define
is given by the first term
ZL/2
U(r)
k−2 fk (T ) = 2 F k (r) exp − dr. (23)
υk (L) ∼ as L → ∞. (18) T
2 f0 (L) 0
On standardised moments of force distribution in simple liquids 5
T T2 ∂
2 k
α f This gives the asymptotic expansion
hEi = + log k 2 2 , (26) √
2 k−2 ∂T fk π T exp[−U(r∗ )/T ]
fk (T ) ∼ p
2U ′′ (r∗ ) (30)
where the first term on the right hand side of equation (26) h i
is the average kinetic energy of our one-atom system. Sub- × Bk,1 T k/2 + Bk,2 T k/2+1 + o T k/2+1 .
stituting equation (8) into the second term on the right hand
side, it can be rewritten as T 2 ∂ (ln f0 )/∂ T . Thus, using equa- as T → 0, where constants Bk,1 and Bk,2 are given by
tion (6), we confirm that the second term on the right hand k/2
side of equation (26) is the average potential energy. Bk,1 = U ′′ (r∗ ) (k − 1)!!
and
E. Low temperature limit Ck,2 (k + 1)!! U (3) (r∗ )Ck,1 (k + 3)!!
Bk,2 = −
|U ′′ (r∗ )|k/2+1 6 |U ′′ (r∗ )|k/2+2
Next, we consider the behaviour of the k-th standardised mo- !
ment of force, αk (T ), given by equation (8), in the low tem- (U ′′ (r∗ ))k/2−2 (k + 3)!! (k + 5)U (3) (r∗ ) (4) ∗
+ −U (r ) .
perature limit, T → 0, which is equivalent to the limit β → ∞. 24 3U ′′ (r∗ )
On standardised moments of force distribution in simple liquids 6
In this section we employ the far field approximation ap- It is useful to introduce a change of coordinates ξ ℓ = qℓ1 − qℓ2
proach introduced in Section III B and we will vary the num- and η ℓ = qℓ1 + qℓ2 for ℓ = x, y, z. We note that r12 is only de-
ber density of the system by changing the size L of the inte- pendent on the ξ ℓ variables, therefore one can trivially inte-
gration domain, which will be given as the three-dimensional grate (34) through the η ℓ variables as the integrand has no
cube [0, L]3 . Using notation introduced in Section II, the dis- dependence on these to obtain
tance between atoms labelled i, j = 1,2, . . . , N positioned at
ZL ZL ZL
qi , q j ∈ R3 is denoted by ri j = qi − q j . Taking
into account L3
fk = F1k (r12 ) exp[−β U(r12 )] dξ x dξ y dξ z ,
the periodic boundary conditions, the distance qi − q j is the 8
−L −L −L
minimum image inter-atomic distance given by
where r12 is the minimum image inter-atomic distance (33).
2 2 2 1/2
|qi − q j | = (qxi − qxj ) + (qyi − qyj ) + (qzi − qzj ) , (33) This integral can be written in terms of standard Euclidean
distance r2 = (ξ x )2 + (ξ y )2 + (ξ z )2 as
where the overline denotes ζ = ζ − L [ζ /L] for ζ ∈ R and [.] ZL/2 ZL/2 ZL/2
rounds a real number to the nearest integer. For an interact- fk = 8 L 3
F1k (r) exp[−β U(r)] dξ , (35)
ing N-body system the dimensionality of the integral given by
0 0 0
equation (7) is 3N. We first present an illustrative calculation
with N = 2 interacting atoms in Section IV A and then we where dξ = dξ x dξ y dξ z .
In order to analyse fk further by
study systems with larger values of N in Section IV B. implementing a far field approximation, we need to make sure
On standardised moments of force distribution in simple liquids 7
10 6
10 4
10 2
10 0
10 -5 10 -4 10 -3 10 -2 10 -1 10 0
FIG. 4. Dependence of kurtosis α4 on density n. Each of the larger atomic systems (N = 8, 64, 512) is simulated over the same domain of
number densities, while the N = 2 system is simulated in a sparser domain. We truncate the results of the N = 2 simulation in the plot, though
the additional data points are used in calculating asymptotic results displayed in Figure 5.
5 800
4
600
3
400
2
200
1
0 0
4 6 8 10 12 0 0.5 1 1.5
FIG. 5. Comparison of the results of N-atom simulations for a range FIG. 6. Dependence of kurtosis α4 on temperature T . Each atomic
of values of the total number of atoms, N, found within the principal system is simulated at approximately the same density n = n0 given
cubic domain. After long time simulation, we compute the asymptotic in Table I.
behaviour αk ∝ n−κ and compare the leading order power scalings
for each system. We compare this with the theoretical result (39)
(denoted with a blue dashed line) that in the limit n → 0 we expect
ier tails and therefore distributions which become increasingly
the universal behaviour κ = k/2 − 1.
leptokurtic.
In Figure 6, we observe that there is a qualitative difference
between the results for N = 2 and larger atom systems. We
given in Table I. We observe that as temperature increases so see a bifurcation for the N = 64, 512 system at some critical
does the kurtosis of the force distribution associated with each temperature Tc ∈ (0.6, 0.65), where a steady increase in kur-
system. This can be explained in terms of the dynamics of the tosis meets a large jump resulting in a rapid increase. This
interacting atom system. If we maintain each system in the difference is due to a clustering mechanism which has been
canonical ensemble, we expect on average that each atom will seen in MD simulations of Lennard-Jones fluids30 . From our
have a kinetic energy equivalent to 3 T /2 (when in reduced results we see that the N = 2 system has missed this behaviour
units). As we increase this target temperature, the atoms be- completely. Snapshots of the N = 512-atom system at some
come more energetic and thus are able to probe closer inter- T = 0.6 < Tc , and T = 0.66 > Tc are displayed in Figure 7.
atomic distances before a large repulsive force overcomes this For T = 0.6, we see a large cluster has formed in the many-
inertial attraction. The range of forces on the tagged parti- atom system. There would be far fewer outlier force results
cle widens as temperature increases and therefore contributes in this case due to the fact that the large majority of atoms
to more outlier results in the distribution - leading to heav- are moving as a collective and effectively have fixed inter-
On standardised moments of force distribution in simple liquids 9
dardised moments of force in Figure 6, though a general in- no closed form for the number of solutions. In particular,
crease in temperature, or decrease in number density, results simplifying equation (A2) by solving equations (A3)–(A4) is,
in an increase in a4 regardless of the temperature/number den- in general, not possible. However, noting the specific prop-
sity domain studied, as shown in Figure 8. erty that F(r∗ ) = 0 = U ′ (r∗ ), we see that all terms that have
α0 6= 0 will vanish when evaluated at this unique minimum
r = r∗ . In particular, we will obtain relatively simple forms
ACKNOWLEDGMENTS of the sum (A2) for m = k + 1 and m = k + 2 by considering
equations (A3)–(A4) with α0 = 0.
This work was supported by the Royal Society [grant number First, let us consider that m = k + 1. Using α0 = 0, there
RGF\EA\180058] and by the Engineering and Physical Sci- is only one solution of equations (A3)–(A4) in non-negative
ences Research Council [grant number EP/V047469/1]. integers, namely α1 = k − 1, α2 = 1 and α3 = α4 = · · · = 0.
Therefore, equation (A2) implies
k−1
Appendix A: Derivation of equations (28) and (29) F k, (k+1) (r∗ ) = C(0, k − 1, 1, 0, . . . , 0) F (1) (r∗ ) F (2) (r∗ ).
The constants used in equation (30), namely Ck,1 and Ck,2 , are Using the general Leibniz rule37 , we evaluate the combina-
given in equations (28) and (29), which can be derived in the torial prefactor as C(0, k − 1, 1, 0, . . . , 0) = k(k + 1)!/2. Sub-
following manner. Using F k (r) = (U ′ (r))k for even values of stituting into Ck,1 = F k, (k+1) (r∗ )/(k + 1)! and using F(r∗ ) =
k and U ′ (r∗ ) = 0, we first note that −U ′ (r∗ ) and that k is an even integer, we obtain formula (28).
k Second, we will consider the case m = k + 2. Using α0 =
F k, k (r∗ ) = k! U ′′ (r∗ ) ,
0, there are two solutions of equations (A3)–(A4) in non-
F k, m (r∗ ) = 0, for m ≤ k − 1, negative integers. The first solution is α1 = k − 1, α2 = 0,
α3 = 1 and α4 = α5 = · · · = 0.The second solution is α1 =
where F k, m
denotes the m-th derivative of F k , i.e. the m-th k − 2, α2 = 2 and α3 = α4 = · · · = 0. Therefore, equation (A2)
derivative of the k-th power of F. Therefore, the first three implies
non-zero terms of the Taylor expansion of F k (r) around r = r∗
are F k, (k+2) (r∗ )
k−1
F k, (k+1) (r∗ )
= C(0, k − 1, 0, 1, 0, . . . , 0) F (1) (r∗ ) F (3) (r∗ )
k ∗ k ′′ ∗
k ∗ k+1
F (r) ≈ (r − r ) U (r ) + (r − r )
(k + 1)! k−2 2
F k, (k+2) (r∗ ) +C(0, k − 2, 2, 0, 0, . . . , 0) F (1) (r∗ ) F (2) (r∗ ) .
+(r − r∗ )k+2 . (A1)
(k + 2)!
Using the general Leibniz rule37 , we evaluate these combina-
Therefore, we have Ck,1 = F k, (k+1) (r∗ )/(k + 1)!
and Ck,2 = torial prefactors as
F k, (k+2) (r∗ )/(k + 2)! and, to derive equations (28) and (29), k
we need to express derivatives F k, m (r∗ ) for m = k + 1 and C(0, k − 1, 0, 1, 0, . . . , 0) = (k + 2)!,
m = k + 2 in terms of derivatives of U(r) at r = r∗ . Using the 6
product rule, the m-th derivative of F k (r) can be, in general, k(k − 1)
C(0, k − 2, 2, 0, 0, . . . , 0) = (k + 2)!.
written as a finite sum of the form 8
k m αi Substituting into formula Ck,2 = F k, (k+2) (r∗ )/(k + 2)! and us-
F k, m
(r) = ∑ C(α0 , α1 , . . . , αm ) ∏ F (i) (r) , (A2) ing F(r∗ ) = −U ′ (r∗ ) and that k is an even integer, we obtain
α0 ,α1 ,...,αm =0 i=0 equation (29). Thus, we have arrived at the the expressions
for Ck,2 and Ck,2 that are used in equation (30).
where F (i) (r) is the i-th derivative of function F(r) and
C(α0 , α1 , . . . , αm ) are constants, many of them equal to zero.
In fact, all terms in the expansion (A2) have multiplicities that Appendix B: Thermostats used in MD simulations
sum to k, that is we can only sum over sequences satisfying
m Considering 3D simulations in Section IV B, we use a Nosé-
∑ αi = k, (A3) Hoover thermostat. Its parameter, originally38 denoted Q, is
i=0 the relaxation time of the thermostat. It is a measure of how
and all terms in the expansion (A2) have m derivatives, that is, strongly the thermostat is attached to the dynamics of the sys-
we have tem. We choose a cautious value of Q = 10 T for each simula-
tion; this linear scaling with T is necessary as we need to more
m
tightly couple the thermostat at lower temperatures in order to
∑ i αi = m, (A4)
accurately maintain the system in the canonical ensemble39 .
i=0
For 1D simulations in Section III, we maintain the canon-
where αi ∈ {0, 1, . . . , k} for i = 0, 1, 2, . . . , m. Equation (A4) ical ensemble at a target (reduced) temperature T by imple-
is of the form of a finite Diophantine equation, which has menting a Langevin thermostat. This is due to problems with
On standardised moments of force distribution in simple liquids 11
ergodicity utilising the Nosé-Hoover thermostat for small sys- 19 J. Jones. On the determination of molecular fields. — II. From the equation
tems40,41 . Here the evolution of the free particle is modelled of state of a gas. Proceedings of the Royal Society A, 106:738 (1924)
20 H. Watanabe, N. Ito and C. Hu. Phase diagram and universality of the
(in reduced units) as42,43
Lennard-Jones gas-liquid system. Journal of Chemical Physics 136, 204102
(2012)
dU p 21 J-P. Hansen and L. Verlet. Phase transitions of the Lennard-Jones system.
ẍ = − − γ ẋ + 2 γ T R(t) , (B1) Physical Review 184:151 (1969)
dx 22 A. Rahman. Correlations in the motion of atoms in liquid argon. Physical
cesses, Cambridge Texts in Applied Mathematics, Cambridge University nealing. Science 220, p671 (1983)
30 N. Yoshii and S. Okazaki. Molecular dynamics study of structure of clusters
Press (2020)
4 H. Ingólfsson et al. The power of coarse graining in biomolecular simula- in supercritical Lennard–Jones fluid. Fluid Phase Equilibria 144(1-2), p225
tions. Wiley Interdisciplinary Reviews: Computational Molecular Science (1998)
31 J. Jung, J. Lee and J. Kim. Cluster growth mechanisms in Lennard-Jones
4(3), p225 (2014)
5 A. Davtyan et al. Dynamic force matching: A method for constructing dy- fluids: a comparison between molecular dynamics and Brownian dynamics
namical coarse-grained models with realistic time dependence. Journal of simulations. Chemical Physics 449, p1 (2015)
32 W. Humphrey, A. Dalke and K. Schulten. VMD - Visual Molecular Dynam-
Chemical Physics 142, 154104 (2015)
6 R. Erban. Coupling all-atom molecular dynamics simulations of ions ics. Journal of Molecular Graphics 14, p33 (1996)
33 A. Schultz and D. Kofke. Erratum: "Comprehensive high-precision
in water with Brownian dynamics. Proceedings of the Royal Society A
472(2186):20150556 (2016) high-accuracy equation of state and coexistence properties for classi-
7 D. Wales. Exploring energy landscapes. Annual Review of Physical Chem- cal Lennard-Jones crystals and low-temperature fluid phases". Journal of
istry 69, p401 (2018) Chemical Physics 153, 059901 (2020)
8 R. Gunaratne et al. On short-range and long-range interactions in multi- 34 S. Stephan et al. Thermophysical properties of the Lennard-Jones fluid:
resolution dimer models. Interface Focus 9 (3), rsfs.2018.0070 (2019) database and data assessment. Journal of Chemical Information and Mod-
9 E. Rolls, Y. Togashi and R. Erban. Varying the resolution of the Rouse model eling 2019 59 (10), 4248 (2019)
35 S. Stephan, J. Staubach and H. Hasse. Review and comparison of equations
on temporal and spatial scales: application to multiscale modelling of DNA
dynamics. Multiscale Modeling and Simulation 15(4), p1672 (2017) of state for the Lennard-Jones fluid. Fluid Phase Equilibria 523, 112772
10 R. Erban. From molecular dynamics to Brownian dynamics, Proceedings of (2020)
36 E. Mastny and J. de Pablo. Melting line of the Lennard-Jones system, infinite
the Royal Society A 470(2167): 20140036 (2014)
11 L. DeCarlo. On the meaning and use of kurtosis. Psychological Methods size, and full potential. Journal of Chemical Physics 127, 104504 (2007)
37 A. Traheem and A.Laradji. Classroom note: a generalization of Leibniz
2(3), p292 (2014)
12 A. Carof, R. Vuilleumier and B. Rotenberg. Two algorithms to compute rule for higher derivatives. International Journal of Mathematical Educa-
projected correlation functions in molecular dynamics simulations. Journal tion in Science and Technology 34(6): 905 (2003)
38 S. Nosé. A molecular dynamics method for simulations in the canonical
of Chemical Physics 140, 124103 (2014)
13 H. Shin et al. Brownian motion from molecular dynamics. Chemical Physics ensemble. Molecular Physics 52(2), p255 (1984)
39 P. H. Hünenberger. Thermostat algorithms for molecular dynamics simu-
375, p316 (2010)
14 R. Erban. Coarse-graining molecular dynamics: stochastic models with lations. In: Dr. Holm C., Prof. Dr. Kremer K. (eds) Springer Advanced
non-Gaussian force distributions. Journal of Mathematical Biology 80, Computer Simulation. Advances in Polymer Science 173, p105 (2005)
40 M. E. Tuckerman et al. Non-Hamiltonian molecular dynamics: generaliz-
p457 (2020)
15 S. Chandrasekhar. Stochastic problems in physics and astronomy. Review ing Hamiltonian phase space principles to non-Hamiltonian systems. Jour-
of Modern Physics 15:1 (1943) nal of Chemical Physics 115, p1678 (2001)
16 A. Gabrielli et al. Force distribution in a randomly perturbed lattice of iden- 41 P. F. Tupper. Ergodicity and the numerical simulation of Hamiltonian sys-
tical atoms with 1/r2 pair interaction. Physical Review E 74:021110 (2006) tems. SIAM Journal on Applied Dynamical Systems 4(3), p563 (2005)
17 G. Rickayzen et al. Single atom force distributions in simple fluids. Journal 42 T. Schlick. Molecular modeling and simulation. Springer (2002)
43 B. Leimkuhler and C. Matthews. Molecular dynamics with determinis-
of Chemical Physics 137, 094505 (2012)
18 A. C. Branka, D. M. Heyes and G. Rickayzen. Pair force distributions in tic and stochastic numerical methods. Springer Interdisciplinary Applied
simple fluids. Journal of Chemical Physics 135, 164507 (2011) Mathematics 39 (2015)