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Lecture 7
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04.06.2012 1
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
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.
E= H = K + U (6.1)
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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
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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.
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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)
δUδP NVT
= k BT 2 (γ V − ρk B ) (6.12)
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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)
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
δPδK NVE
= δPδU NVE
= Nk B2T 2 V (1 − 3Vγ V 2CV ) (6.18)
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
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)
µVT
(
CV = 32 Nk B + 1 k BT 2 δU 2
µVT
− δUδN
2
µVT δN 2 µVT
) (6.25)
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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).
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
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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
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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
µ = k BT ln (ρΛ ) + 4π ∫ ξ ∫ r 2υ (r ) g (r ; ξ )dr
1 ∞
3
(6.32)
0 0
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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)
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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)
• so that
or
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• The computation of the CAB (t) may be thought of as a two step
process:
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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.
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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
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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.
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
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.
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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
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.
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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
A G V G V P G V G V P G V G V P G V G
N N 1st minor 27 -helix
N N
G G diagonal G G ∆i=2
V V
G G V V
P P G G
V V P P
Main minor V V
G G Main minor
diagonal G G
Nitrogen
V V
diagonal
Nitrogen
G G V V
P P G G
V V P P
G G V V
V V G G Disordered
V V
G G
G G
structure
P P
N-terminus
V V P P
G G V V
V V G G
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 Main major A G V G V P G V G V P G V G V P G V G β-sheet
Oxygen diagonal
N-terminus C-terminus 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)
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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)
∞
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:
δP (t ) = P (t ) − P = P (t ) − P (6.52b)
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
2tλT =
V
k BT 2
(
δε α (t ) − δε α (0)
2
) (6.55)
∑ r α (ε )
1
δε α = i i − εi (6.56)
V i
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• The term
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• 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.
⋅2 (6.59)
= vi −
2 1
2
vi t 2
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• 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
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• There are some other correlation functions of interest in computer
simulations which we will discuss here very briefly.
I (k , t ) = N −1 ρ (k , t )ρ (− k ,0) (6.63)
• All these functions may be divided into parts due to “self” (i.e.
single-particle) motion and due to “distinct” (i.e. collective) effects.
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• 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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