Molecular Dynamics Simulations:

from Basics to Applications.

Lecture 7

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 Content of the Lecture 7:
1. Simple thermodynamic averages

2. Fluctuations
• Specific heat capacities
• Thermal expansion coefficient
• Isothermal compressibility
• Thermal pressure coefficient

3. Structural quantities
• Pair distribution function
• Structure factor

4. Time correlation functions and transport coefficients

• Diffusion coefficient

5. Structure of biomolecules.
• Radius of gyration
• Secondary structure
• Intra-molecular hydrogen bonds.

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 Simple thermodynamic averages.

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 • The basic thermodynamic properties of the system can be
calculated in any convenient ensemble.

• These functions are usually derivatives of one of the characteristic

thermodynamic functions Ψens.

• The kinetic, potential and total internal energies can be calculated

using the phase function shown in lecture 1:

E= H = K + U (6.1)

• The kinetic energy is a sum of contributions from individual

particles momenta, while the calculation of the potential energy
involves summing over all pairs, triplets etc. of molecules,
depending on the complexity of the function.

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 • The temperature and the pressure may be calculated using the
virial theorem, which we write here in form of “generalized
equipartition”:
pk ∂H ∂pk = k BT (6.2 a)

qk ∂H ∂qk = k BT (6.2 b)
• So the instantaneous “kinetic temperature” whose average is
equal to T, can be defined as:
N
1
T = 2 K 3Nk B = ∑ pi
2
mi (6.3)
3 Nk B i =1

• And the instantaneous pressure whose average is equal to P, can

be defined as follows”
P = ρk BT + W V =P id
+P ex
(6.4)

• where W is the “internal virial”:

1 N
W = ∑ r i fiinter (6.5)
3 i =1
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 • Quantities such as ‹N› and ‹V› can be easily calculated in the
simulation of ensembles in which these quantities vary, and
derived functions such as enthalpy ‹H›, are easily calculated from
the above.

• The direct approach to calculate entropy-related (“statistical”)

properties such as the Helmholtz (A) and Gibbs functions (G),
the chemical potential (µ) and the entropy (S) it self, is to
perform simulation in grand canonical ensemble in which µ or
other quantity is specified.

• However, as we have already seen, there are some technical

difficulties associated with the simulations in the grand canonical
ensemble.

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 • It should be also stated, that it is difficult to calculate these
properties in other common ensembles, because they related to
the partition function Q and not to its derivatives. So we need to
calculate Q summing over all the states of the system.
• It might seem that to estimate excess statistical properties we
could use the following formula:

exp( A ex
k BT ) = Q ex −1
NVT = exp(U k BT ) NVT
(6.6)

• But the distribution ρNVT will be very sharply peaked around the
largest values of exp(-U/kBT), i.e. where exp(U/kBT) is
comparatively small.
• Consequently, any simulation technique that samples according to
the equilibrium distribution will be bound to give a poor estimate of
A by this route.
• Special sampling techniques have been developed to evaluate
averages of this type and we will discuss them in the next
lectures.
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 Fluctuations.

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 • Now, we will discuss the information that can be obtained from the
root mean square (RMS) fluctuations.

• The most interesting quantities are:

– the constant volume specific heat capacity CV = (∂E ∂T )V
– the constant pressure specific heat capacity C P = (∂H ∂T )P

– the thermal expansion coefficient α P = −V −1 (∂V ∂T )P

– the isothermal compressibility βT = −V −1 (∂V ∂P )T

– the thermal pressure coefficient γ V = (∂P ∂T )V
• and the adiabatic (constant S) analogues of last three.

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 • Partially, formulas for these quantities can be obtained from the
standard theory of fluctuations Landau and Lifshitz (1980).
• But, in computer simulations we have to be careful to distinguish
between properly defined mechanical quantities such as the
energy, or Hamiltonian, H, the kinetic temperature T or
instantaneous pressure P, and thermodynamic concepts T and P,
which can be only described as the ensemble averages or the
parameters defining the ensemble.
• Thus, to calculate CV in the canonical ensemble we can simply
use a standard formula:

σ 2 (E ) = δE 2 = k BT 2CV
• Whereas, since P is not the same as P, we can not calculate
isothermal compressibility βT using the analogous simple formula:

σ 2 (P ) = δP 2 = k BT VβT

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 • So we will start with the canonical ensemble. As just mentioned,
the specific heat is given by fluctuations in the total energy:
δH 2 NVT
= k BT 2CV (6.7)
• We can divide it into the kinetic and the potential contributions
which are uncorrelated (i.e. ‹δKδU›NVT=0):
δH 2 NVT
= δU 2
NVT
+ δK 2
NVT
(6.8)

• The ideal gas part of the specific heat capacity can be easily
calculated from the kinetic part, for example for the system of N
atoms:

δK 2 =
3N
(k BT )2 = 3N 2β 2 ⇒ CVid = 32 Nk B (6.9)
NVT 2
• And the constant volume specific heat capacity, can be calculated
as follows:
δU 2
δU 2 = k BT 2 (CV − 32 Nk B ) ⇒ CV = NVT
2
+ 32 Nk B (6.10)
NVT k BT
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 • Consideration of the cross-correlation of the potential energy and
the virial fluctuations will give us an expression for the thermal
pressure coefficient γV:

δUδW NVT
= k BT 2 (Vγ V − Nk B ) (6.11)

• And in terms of pressure function defined in eq. (6.4) we can write

for a system of N atoms:

δUδP NVT
= k BT 2 (γ V − ρk B ) (6.12)

• Equation (6.12) also applies if P is replaced by P’ or by Pex, which

is more likely to be available in a constant-NVT Monte Carlo
simulations.

• Similar formulas may be derived for the molecular systems.

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 • If we want to consider fluctuations of the virial itself, we have to
define a further “hyper-virial” function:
X = 19 ∑∑∑∑ rij ⋅ ∇ rij rkl ⋅ ∇ rkl U( )( ) (6.13)
i j >i k l >k
Intermolecular
• Which becomes for a pairwise additive potential,
virial
dw(r )
X= 1
9 ∑∑ x(rij ) where x(r ) = r
i j >i dr
(6.14)

• It is then easy to show that

δW 2 NVT
(
= k BT Nk BT + W NVT
− βT−1V + X NVT
) (6.15)
or
k T  2 Nk BT X 
δP = B  −β +−1

 3V + P
2 NVT
(6.16)
NVT V NVT T
V 
 
• Despite the fact the ‹X› is a non-thermodynamic quantity, it can
be evaluated in computer simulation, and so eqns. (6.15) and
(6.16), provide a route to isothermal compressibility βT.
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 • All fluctuation expressions can be derived for the micro-canonical
ensemble using the formula for the transformation between
different ensembles and the fact that the values of simple
averages remains unchanged by this transformation due to
equivalence of ensembles.
• Specific heat in micro-canonical ensemble may be obtained from
the fluctuations in the separate potential and kinetic components:
δU 2 = δK 2 = 32 Nk B2T 2 (1 − 3Nk B 2CV ) (6.17)
NVE NVE

• Cross-correlation of the pressure fluctuations and the kinetic

energy yields the thermal pressure coefficient:

δPδK NVE
= δPδU NVE
= Nk B2T 2 V (1 − 3Vγ V 2CV ) (6.18)

• The expression for fluctuations of P in the micro-canonical

ensemble gives the isothermal compressibility:
k BT  2 Nk BT X 
δP =  − β + TVγ
−1

 3V + P CV +
2 2 NVE
NVE T V  (6.19)
NVE V  V 
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 • Conversion from the canonical to the isothermal-isobaric
ensemble can be easily done. Most of formulas of interest are
very simple since they involve well-defined mechanical quantities.

• At constant T and P, both volume and energy fluctuations may

occur. The volume fluctuations are related to the isothermal
compressibility βT,

δV 2 NPT
= Vk BTβT (6.20)
• The formula for the specific heat may be obtained by calculating
the “instantaneous” enthalpy,

δ (H + PV ) = k BT 2 C P
2
(6.21)
NPT

• The thermal expansion coefficient may be calculated from the

cross-correlation of “enthalpy” and volume:

δVδ (H + PV ) NPT
= k BT 2Vα P (6.22)

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 • In the grand canonical ensemble, energy, pressure and number of
particles fluctuate. The number of particle fluctuations yield
isothermal compressibility:
δN 2 µVT
(
= k BT (∂N ∂µ )VT = N 2 V k BTβT ) (6.23)

• The formula for specific heat is obtained by considering a function:

δ (H − µN ) = k BT 2CµV = k BT 2 [∂ (H − µN ) ∂T ]µV (6.24)

2

µVT

• And the usual specific CV (i.e. CNV) is obtained by thermodynamic

manipulations:

(
CV = 32 Nk B + 1 k BT 2 δU 2
µVT
− δUδN
2
µVT δN 2 µVT
) (6.25)

• The thermal expansion coefficient may be derived in the same way

PβT δUδN µVT

2
δU µVT
δN 2 µVT
αP = − 2
+ 2 2
(6.26)
T Nk BT N k BT
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 Structural quantities.

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 • The structure of the simple mono-atomic fluid can be
characterized by a set of distribution functions for the atomic
positions, the simplest of which is the pair distribution function
g2(ri,rj), or g2(rij), or simply g(r).

• This function gives the probability of finding a pair of atoms a

distance r apart, relative to the probability expected for a
completely random distribution at the same density.

• To define g(r), we have to integrate the configurational distribution

function over the positions of all atoms except two, incorporating
the appropriate normalization factor. So in the canonical ensemble:

N ( N − 1)
g (r1 , r2 ) = 2 ∫ dr3dr4 ...drN exp(− βU (r1 , r2 ,...rN ) ) (6.27)
ρ Z NVT
• Obviously the choice of i = 1, j = 2 is arbitrary in a system of
identical atoms.

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 • An equivalent definition takes an ensemble average over pairs:

g (r ) = ρ ∑∑ δ (r )δ (r − r) ∑∑ δ (r − r )
V
2
i j = 2 ij (6.28)
i j ≠i N i j ≠i

• This last form may be used in the evaluation of g(r) by computer

simulation; in practice, the delta function is replaced by a function
which is non-zero in a small range of separations, and a
histogram is compiled of all pair separations falling within each
such range.

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 • The pair distribution function is useful, not only because it
provides insight into the liquid structure, but also because the
ensemble average of any pair function may be expressed in the
form:

a (ri , r j ) ∫ dr dr g (r , r )a(r , r )
1
= 2 i j i j i j (6.28)
V

or

A = a (
∑∑ i j
r , r ) = N ρ ∫ a ( r ) 1
g
2 ( r )
∞
4
0
π 2
dr (6.29)
i j >i

• The later expression can be useful if we want to obtain such

properties as energy, pressure of chemical potential.

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 • For example we may write the energy (assuming pair additivity)
∞
E = (3 2)Nk BT + 2πNρ ∫ r 2υ (r ) g (r )dr (6.30)
0
• or the pressure
∞
PV = Nk BT − (2 3)πNρ ∫ r 2 w(r ) g (r )dr (6.31)
0

• although in practice a direct evaluation of these quantities, as

discussed above, will usually give more accurate results.
• The relation of chemical potential to the pair distribution function
g(r) can be written in following way:

µ = k BT ln (ρΛ ) + 4π ∫ ξ ∫ r 2υ (r ) g (r ; ξ )dr
1 ∞
3
(6.32)
0 0

• As usual with the chemical potential, there is a twist: the formula

involves a pair distribution g(r,ξ) which depends upon a parameter
coupling the two atoms, and it is necessary to integrate over this
parameter.
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 • The definition of pair distribution function may be extended to the
molecular case when the function g(rij,Ωi,Ωj) depends upon the
separation between, and the orientations of molecules.
• Exist a number of approaches which give partial description of
orientational ordering:
– Sections through g(rij,Ωi,Ωj) are calculated as a function of rij for fixed
relative orientations
– g(rij,Ωi,Ωj) can be represented as a spherical harmonic expansion,
where the coefficients are functions of rij.
– a set of site-site distribution functions gab(rab), can be calculated in the
same way as the atomic g(r) for each type of site.
• The later case is most simple, however, the number of independent
gab(rab) functions will depend on the complexity of the molecule. For
example in a three-site OCS, the isotropic liquid is described by six
independent gab functions (for OO, OC, OS, CS, CC, SS distances).
• Although these distribution functions contain less information than
g(rij,Ωi,Ωj), they have the advantage of being directly related to the
structure factor of the liquid, the experimentally observable
properties.
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 • Now we will turn to the definition of quantities that depend upon
the wavevector rather than on position.
• In a simulation with periodic boundaries, we a restricted to
wavevectors that are commensurate with the periodicity of the
system, i.e. with the size of simulation box.
• Specifically, in a cubic box, we may examine fluctuations for
which:
k = (2π L )(k x , k y , k z ) (6.33)

• where L is the box length, and kx, ky, kz are integers.

• One quantity of the interest is the spatial Fourier transform of the

number density:
N
ρ (k ) = ∑ exp(ik ⋅ ri ) (6.34)
i =1

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 • Fluctuations in ρ(k) are related to the structure factor S(k)

S (k ) = N −1 ρ (k )ρ (− k ) (6.35)

• which may be measured by neutron or X-ray scattering

experiments.
• Thus S(k) describes the Fourier components of density
fluctuations of the liquid.

• The structure factor S(k) related, through a three-dimensional

Fourier transform to the pair distribution function
∞
2 sin kr
S (k ) = 1 + ρh(k ) = 1 + ρgˆ (k ) = 1 + 4πρ ∫ r
ˆ g (r )dr (6.36)
0 kr
• where we have introduced the Fourier transform of the total
correlations function h(r) = g(r) – 1, and ignored a delta function
contribution at k=0.
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 Time-correlation functions and
transport coefficients.

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 • Correlation between two different quantities A and B are
measured in the usual statistical sense, via the correlation
coefficient cAB
cAB = δAδB σ ( A )σ (B ) (6.37)

• Schwartz inequalities guarantee that the absolute value of cAB

lies between 0 and 1, with values close to 1 indicating a high
degree of correlation.
• We can evaluate correlation coefficient at two different times, the
resulting quantity is a function of the time difference t, and called
“time correlation function”.
• The identical phase function cAA (t), called an “autocorrelation
function” are of great interest in computer simulations because:
– They give a clear picture of the dynamics in a fluid;
– Their time integrals tA may often be related directly to the microscopic
transport coefficients;
– Their Fourier transforms ĉAA (ω) may often be related to experimental
spectra.
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 • We will give only few comments to the “time correlation functions”.

• The non-normalized correlation function is defined

CAB = δA (t )δB (0 ) ens = δAΓ(t )δBΓ(0 ) ens (6.38)

• so that

cAB (t ) = CAB (t ) σ (A )σ (B ) (6.39)

or

cAA (t ) = CAA (t ) σ 2 ( A ) = CAA (t ) CAA (0 ) (6.40)

• The CAB (t) is different for different ensembles, and we can

transform it using a formula for the transformation between
various ensembles.

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 • The computation of the CAB (t) may be thought of as a two step
process:

1. First, we have to select initial state points Γ(0), according to

desired distribution ρens(Γ), over which we will subsequently
average.
2. Second, we must evaluate Γ(t). This means solving the true
(Newtonian) equation of motion.

• By this means, time-dependent properties may be calculated in

any ensemble. In practice, the mechanical equations of motion
are almost always used for both purpose, i.e. we use molecular
dynamics to calculate time correlation functions in the micro-
canonical ensemble.
• Some attention have to be paid to the question of the ensemble
equivalence, since the link between correlation functions and
transport coefficients is made through linear response theory,
which can be carried out in virtually any ensemble.

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 • The transport coefficients are defined in terms of the response of
a system to a perturbation. For example, the diffusion coefficient
relates the particle flux to a concentration gradient, while a shear
viscosity is a measure of the shear stress induced by an applied
velocity gradient.

• By introducing such perturbations into the Hamiltonian, or directly

into the equations of motion, their effect on the distribution
function ρens can be calculated.

• Generally we produce a time-dependent, non-equilibrium

distribution ρ(t) =ρens+ δρ(t). Hence, any non-equilibrium
ensemble average may be calculated.

• By retaining the linear terms in the perturbation, and comparing

the equation for the response with a macroscopic transport
equation, we may identify the transport coefficient.

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 • This is usually the infinite time integral of an equilibrium time
correlation function of the following form:
∞ • •
γ = ∫ dt A (t ) A (0) (6.41)
0
• where γ is the transport coefficient and A is the variable
appearing in the perturbation term in Hamiltonian
• There is also “Einstein relation”, which is associated with any
expression of this kind

2tγ = (A (t ) − A (0))2 (6.42)

• which holds at large t, compared to the correlation time of A. The
connections between eqns. (6.41) and (6.42) can be easily
established by integration by parts
• Please keep in mind, that only a few genuine transport
coefficients exist, i.e. for only a few “hydrodynamic” variables A
eqns. (6.41) and (6.42) give a non-zero γ.

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 • In computer simulations, transport coefficients may be calculated
from equilibrium correlation functions, or using Einstein relation.
• Now we will discuss the equations for calculating thermal
transport coefficients in the micro-canonical ensemble, for a
system compose of N identical particles.

• The diffusion coefficient D is given (in three dimension) by

∞
D= 1
∫
3 0 dt v i (t ) ⋅ v i (0 ) (6.43)

• where vi(t) is the center-of-mass velocity of a single molecule.

• The corresponding Einstein relation, valid at a long times, is

2tD = ri (t ) − ri (0 )
1 2
3 (6.44)
• Please note that in the calculation of the eqn. (6.44) it is
important to switch from one periodic image to another.

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 Translational dynamics of Na+ ions.
Time dependence of the Dependence of long-range ion
mean-square displacement of ions mobility Dτ on the hydration level Γ

0.10
60 IV
III

2 -1
0.08

Dτ / 10 m s
I II
2

Γ = 30
<r > / A

-9
40 0.06
2

0.04
20

0.02
Γ = 12

0 100 200 300 400 500 600 12 14 16 18 20 22 24 26 28 30

t / ps Γ
r2(τ + ∆) −r2 (τ −∆) τ = 350 ps
Dτ = ∆ = 150 ps
2d∆ d=3
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 Structure of biomolecules.

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 Radius of gyration.
• Radius of gyration, Rg, is the measure of the size of the
object or an ensemble of points. It is calculated as the
root mean square distance of the objects’ parts from its
center of mass.

∑ (r − rc.o.m. )
1
Rg =
2
k
N k =1

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 T=380 K

Rg=6.2 Å
T=340 K

T=300 K

Rg=8.5 Å

T=280 K

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 Secondary structure elements.
• The structure of proteins frequently decomposed
into primary, secondary, tertiary and quaternary
structure.

• There are three main motives in protein secondary

structure: α-helix, β-sheet, and random coil.

• However exist a large variety of secondary

structure elements, that a not so common and can
be found only in particular proteins, among them:
– 27-helix, 310 helix, π-helix, poly-proline helix
– β-turns

• Secondary structure elements can be described

with help of Ramachandran plots, where torsion
angles for C’-N-Cα-C’ (Φ) and N-Cα-C’-N (Ψ) are
plotted.

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 -120 -60 0 60 120 -120 -60 0 60 120

i+1
et

β-turn II
he

120
PPII 120 120 120
-s
Β

R
60 60 60 60
27

i+
i+2
ψ

ψ
0 0 0 0

2
R
310
-60 -60 -60 -60
R α R
β-turn I
i+1
Π
-120 -120 -120 -120

-120 -60 0 60 120 -120 -60 0 60 120

ϕ ϕ

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 β-turn type II β-turn type I

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 Intra-molecular hydrogen bonds.
• A hydrogen bond is the attractive interaction of a
hydrogen atom with an electronegative atom, such
as nitrogen, oxygen, fluorine or sulfur, that comes from
another molecule or chemical group.

• A hydrogen atom attached to a relatively electronegative

atom is a hydrogen bond donor.

• An electronegative atom such as fluorine, sulfur,

oxygen, or nitrogen is a hydrogen bond acceptor,
regardless of whether it is bonded to a hydrogen atom or
not.

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 α - helix β - sheet

α < 60°
N H O C

r = 3.5 Å

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 4th minor 3rd minor 2nd minor
diagonal α-helix
diagonal diagonal Π-helix 310 -helix
∆i=4
∆i=5 ∆i=3
C-terminus

A G V G V P G V G V P G V G V P G V G
N N
G G
V V
G G
P P
V V
G G
Nitrogen
A G V G V P G V G V P G V G V P G V G
1st minor 27 -helix
N N
diagonal G G ∆i=2
V V
G G
P P
Main minor V V
Main minor
diagonal G G

V V
diagonal

Nitrogen
G G
P P
V V
G G
V V
G G
P P
N-terminus
V V
G G
P P
V V
G G Disordered
V V
G G
structure

V V
G G
V V
G G
A G V G V P G V G V P G V G V P G V G
Oxygen
N-terminus C-terminus
P P
V V
G G
V V
G G
Main major A G V G V P G V G V P G V G V P G V G β-sheet
diagonal
Oxygen

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 • The shear viscosity is given by:
∞
dt Pαβ (t )Pαβ (0 )
V
η= ∫ (6.45)
k BT 0
• or by

2tη =
V
k BT
( J (t ) − J (0))
αβ αβ
2
(6.46)
• Here
1 
Pαβ =  ∑ piα piβ mi + ∑ riα f iβ  (6.47)
V i i 
or
1 
Pαβ =  ∑ piα piβ mi + ∑∑ rijα f ijβ  (6.48)
V i i j >i 
• is an off-diagonal (α≠β) element of the pressure tensor.

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 • The
1
J αβ =
V
∑ rα p β
i
i i (6.49)

• The negative of the Pαβ is often called the stress tensor.

• These properties are multi-particle, properties of the system as a

whole, and so no additional averaging over the N particles is
possible.

• Consequently η is subjected to much greater statistical

imprecision than D. Some improvement can be made by
averaging over different components, αβ=xy, yz, zx, of Pαβ

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 • The bulk viscosity is given by a similar expression:

∞
dt δPαα (t )δPββ (0 ) =
V
ηV =
9 k BT
∑
αβ
∫ 0

∞
dt δP (t )δP (0 )
V
=
k BT ∫
0
(6.50)

• where we sum over α, β = x, y, z and note that

1
P = ∑ Pαα
3 α
• Rotational invariance leads to the equivalent expression

∞
dt δPαα (t )δPαα (0 )
V
ηV + η =
4
3 ∫ (6.51)
k BT 0

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 • The diagonal stresses have to be evaluated with care, since a
non-vanishing equilibrium average must be subtracted:

δPαα (t ) = Pαα (t ) − Pαα = Pαα (t ) − P (6.52a)

δP (t ) = P (t ) − P = P (t ) − P (6.52b)

• with Pαα given by expression similar to eqn. (6.48)

• The corresponding Einstein relation is:

2t (ηV + η ) =
4
3
V
k BT
( J (t ) − J (0) − Pt )
αα αα
2
(6.53)

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 • The thermal conductivity λT can be written as follows:

∞
dt jαε (t ) jαε (0)
V
λT = ∫ (6.54)
k BT 2 0

• The Einstein relation is:

2tλT =
V
k BT 2
(
δε α (t ) − δε α (0)
2
) (6.55)

• Here, jαε is a component of the energy current, that is the time

derivative of:

∑ r α (ε )
1
δε α = i i − εi (6.56)
V i

Analysis of trajectories
04.06.2012 46
 • The term

∑ rαi εi makes no contribution if ∑ rα = 0

i
i
i

• as in a normal one-component MD simulation.

• In calculation of the energy per molecule εi, the potential energy of

two molecules (assuming pairwise potentials) is taken to be divided
equally between them:

ε i = pi2 2mi + 12 ∑υ (rij ) (6.57)

j ≠i

• Please note, the expression for ηV and λT are ensemble-

dependent and the above equations hold for the micro-
canonical case only.

Analysis of trajectories
04.06.2012 47
 • Transport coefficients are related to the long-time behavior of
correlation functions.
• Short-time correlations, on the other hand, may be linked with
static equilibrium ensemble averages, by expanding in a Taylor
series.

• For example, the velocity of particle i may be written

⋅ ⋅⋅
v i (t ) = v i (0 ) + v i (0 )t + 12 v i (0 )t 2 + ... (6.58)

• Multiplying by vi(0) and ensemble averaging gives us:

⋅⋅
v i (t )v i (0) = vi + v i v i t 2 + ... =
2 1
2

⋅2 (6.59)
= vi −
2 1
2
vi t 2

• Thus the short-time velocity auto-correlation function is related to

the mean square acceleration, i.e. to the mean square force.

Analysis of trajectories
04.06.2012 48
 • This behavior can be used to define the Einstein frequency ωE

v i (t )v i (0 ) = vi
2
(1 − 1
2 ω E2 t 2 + ...) (6.60)
• The analogy with Einstein model, of an atom vibrating in the mean
field of its neighbors, with frequency ωE in the harmonic
approximation becomes clear when we replace the mean square
force by the average potential curvature using

f iα2 = − f iα ∂U ∂riα = k BT ∂ 2U ∂riα2 (6.61)

• And the result is:

f iα2 1
ω =
2
E 2 2
= ∇ r2i U (6.62)
m v
i i
3mi

• This may be easily evaluated in computer simulation for a pair-

wise potential.

Analysis of trajectories
04.06.2012 49
 • There are some other correlation functions of interest in computer
simulations which we will discuss here very briefly.

• The generalization of eqn. (6.35) to the time domain gives the

intermediate scattering function I(k,t)

I (k , t ) = N −1 ρ (k , t )ρ (− k ,0) (6.63)

• The temporal Fourier transform of this function, the dynamic

structure factor S(k,ω), may be measured by inelastic neutron
scattering.

• Spatially Fourier-transforming I(k,t) yields the van Hove function

G(r,t), a generalization of g(r) which measures the probability of
finding a particle at position r at time t, given that a particle was at
the origin of coordinates at time 0.

• All these functions may be divided into parts due to “self” (i.e.
single-particle) motion and due to “distinct” (i.e. collective) effects.
Analysis of trajectories
04.06.2012 50
 • For a system of rigid molecules, the angular velocity ωi plays a
role in reorientational dynamics analogous to that of vi in
translation.
• The angular velocity correlation function ‹ωi(t) ωi(0)› may be used
to describe rotation. Time-dependent orientational correlations may
be defined as straightforward generalizations of the quantities seen
earlier.
• For a linear molecule, the time correlation function of rank-l
spherical harmonics is:
cl (t ) = 4π Ylm (Ω i (t ))Ylm* (Ω i (0 )) = Pl (cos δγ (t )) (6.64)
• where δγ(t) is the magnitude of the angle turned through in time t.
Note that there are 2l+1 rank-l functions, all identical in form,
corresponding to different values of m.
• Please note, that the first-rank auto-correlation functions may be
related to infra-red absorption, and second-rank functions to light
scattering. Functions of all ranks contribute to inelastic neutron
scattering spectra from molecular liquids.
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04.06.2012 51