Introduction To World of MD Simulations

Understanding
Molecular Simulations
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Why Molecular Simulations
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Paul Dirac, after completing his formalism of quantum mechanics:
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“The rest is chemistry…”.
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This is a heavy burden the shoulders of “chemistry”:
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This is a heavy burden the shoulders of “chemistry”:
The “rest” amounts to the quantitative description of the world around us

and the prediction of all every-day phenomena ranging from the
chemical reactions of small molecules to the integrated description of
living organisms.
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Concept of Molecular Simulations
for a given intermolecular potential

“exactly” predict the thermodynamic and
transport properties of the system
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We assume the
interactions between
the particles are known!
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Exact = in the limit of
infinitely long simulations the
error bars can be made
infinitely small

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Pressure
Heat capacity
Heat of adsorption
Structure
….
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Diffusion coefficient
Viscosity
…
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If one could envision
an experimental
system of these
particles that interact
for a given intermolecular
potential
with the potential.
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“Can we predict the
THE question: macroscopic properties of
(classical) many-body systems?”
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NEWTON says: yes, my F=ma gives
the future time evolution of the
system
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system
LAPLACE says: in principle yes,

provided that we know the
position, velocity and interaction of
all molecules, then the future
behavior is predictable,..
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system

BOLZMANN says: yes, just solve my phase space integral

(for static properties)
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system


both approaches should lead to the same results:

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system


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both approaches should lead to the same results: But......
.... there are so many molecules....
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...making these approaches untractable.
What was the alternative at the time ?
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1. Smart tricks (“theory”)

Only works in special cases: the Ising model: the ideal gas, etc etc
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1. Smart tricks (“theory”)

Only works in special cases: the Ising model: the ideal gas, etc etc
2. Constructing a model (“molecular lego”).
J.D. Bernal’s ball-bearing model Watson and Crick’s model of

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The computer age
The computer age (1953…)
Berni Alder
Mary-Ann Mansigh
Tom Wainwright
With computers we can follow the behavior of hundreds to

Withhundreds
computers of we can follow
millions the behavior of hundreds to hundreds
of molecules.
of millions of molecules.
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Increment of power since 1950’s
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Performance
Super Development
computer performance development
!"%%4'()*+,%
100 Pflop/s
100000000
10 Pflop/s 2#3%4'()*+,%
10000000
1 Pflop/s
1000000
100 Tflop/s 56/%

100000 -0%1'()*+,%
10 Tflop/s
10000 780%
1 Tflop/s 0#0$%1'()*+,%
1000 6-8 years
100 Gflop/s
100 78!..%
!"#$%&'()*+,%
My Laptop (12 Gflop/s)
10 Gflop/s
10
1 Gflop/s My iPad2 & iPhone 4s (1.02 Gflop/s)
1
-..%/'()*+,%
100 Mflop/s
0.1
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Speed of MD simulations
1012
Psec/atom/CPU h
106
1
1950 1970 1990 2010
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Speed of MD simulations
1012
ab-initio MD is
invented
Psec/atom/CPU h
106
1
1950 1970 1990 2010
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Uses of Molecular Simulations
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• Mimic the real world:
– Predicting properties of (new) materials
– Computer ‘experiments’ at extreme conditions
– Understanding phenomena on a molecular scale
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• Mimic the real world:
– Predicting properties of (new) materials
– Computer ‘experiments’ at extreme conditions
– Understanding phenomena on a molecular scale
• Model systems
– test theory using same simple model
– explore consequences of model
– explain poorly understood phenomena in terms of
essential physics
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Properties of materials
Critical properties of long chain hydrocarbons
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Properties of materials
Critical properties of long chain hydrocarbons
To predict the thermodynamic properties (boiling points)

of the hydrocarbon mixtures it is convenient to know the critical
points of the hydrocarbons.
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Hydrocarbons intermolecular potential
United-atom model CH2 CH2

– Fixed bond length
CH3
– Bond-bending CH2 CH3
– Torsion
– Non-bonded: Lennard-Jones
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Vapour-liquid
equilibria
13
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Vapour-liquid
equilibria
Computational issues:
13
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Vapour-liquid
equilibria
• How to compute
vapour-liquid
equilibrium?
13
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Vapour-liquid
equilibria
• How to compute
vapour-liquid
equilibrium?
• How to deal with long
chain hydrocarbons?
13
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Vapour-liquid
equilibria
Course on Free Computational issues:
Energies and Phase • How to compute
Equilibrium vapour-liquid
equilibrium?
chain hydrocarbons?
13
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Vapour-liquid
equilibria
Course on Free Computational issues:
Energies and Phase • How to compute
Equilibrium vapour-liquid
equilibrium?
chain hydrocarbons?
Course on CBMC:
configurational-bias
Monte Carlo
13
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Properties at extreme conditions
• Carbon phase behavior at very high pressure and temperature
• Empirical pair potential depending on carbon coordination
coordination number
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Properties at extreme conditions
• Carbon phase behavior at very high pressure and temperature
• Empirical pair potential depending on carbon coordination
coordination number
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Understand molecular processes
• Protein conformational change with Molecular dynamics
• Empirical potential, including bonds, angles dihedrals
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Course on MD
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• Transition path sampling
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Course on
rare events
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Leads to insight and

new hypotheses
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Testing theories with simple models
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In the 1950‘s an important question arose: Is an attractive interaction
always required to form a solid phase?
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YES:
– Because theories (up to then) predict that attractions are needed for vapour-
liquid equilibrium and thus why not for solids
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YES:
MAYBE NOT:
– These theories do not apply to solids
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YES:
MAYBE NOT:
HOWEVER:
– There no are molecules with only repulsive interactions
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YES:
MAYBE NOT:
HOWEVER:
So how to test the hypothesis that molecules with only repulsive
interaction can freeze?
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YES:
MAYBE NOT:
HOWEVER:
interaction can freeze?
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YES:
MAYBE NOT:
HOWEVER:
Your hypothesis
interaction is
can freeze?
WRONG it disagrees
with the experiments
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My hypothesis is
always required to form a solid phase? RIGHT: but this
YES: experimentalist refuses
to usearemolecules
– Because theories (up to then) predict that attractions that
needed for vapour-
liquid equilibrium and thus why not for solids do not have any
MAYBE NOT: attractive interactions
HOWEVER:
Your hypothesis
interaction is
can freeze?
WRONG it disagrees
with the experiments
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Simulation of hard spheres
An older Alder
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• Bernie Alder et al. carried out

Molecular Dynamics simulations of
the freezing of hard spheres
An older Alder
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• But, …. did the scientific
community accept this computer
results as evidence …?
An older Alder
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• … during a New Jersey conference
in 1957 it was proposed to vote on
it …
An older Alder
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• … during a New Jersey conference
in 1957 it was proposed to vote on
it …
• … and it was voted against the
results of Alder!
An older Alder
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Experiments are now possible
.. not on molecules but on colloids
from :Yethiraj and van Blaaderen

Nature 421, 513-517 (2003)
and show that hard spheres indeed crystallize at high density
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Explore consequences of model
• Trans membrane peptides
• Coarse-grained model of a membrane to study the interactions

between peptides in a membrane
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Course on
coarse graining
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Understanding in terms of essential physics
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• Protein folding is complex:
explicit MD intractable
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• Make simple lattice model with

essential physics of proteins
– polymer connectivity
– heteropolymer sequence
– attraction/repulsion
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• MC simulation yields understanding
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• MC simulation yields understanding
Course on
lattice models
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The limits of Molecular Simulation
• Brute-force simulations can never bridge all the scales between
microscopic (nanometers/picoseconds) and macroscopic (cells,
humans, planets).
• Need different levels of

description (“coarse
graining”) - and we need
input from experiments
at many different levels
to validate our models.
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The limits of experiments
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• Increasingly, experiments generate far more data than humans can digest.
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• Result: “Experulation” or “Simuriment”.
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• Result: “Experulation” or “Simuriment”.
• Simulations are becoming an integral part of the analysis of experimental

data.
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Understanding Molecular Simulation
Molecular simulations are based on the framework of statistical
mechanics/thermodynamics
Hence:
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Understanding Molecular Simulation
Molecular simulations are based on the framework of statistical
Hence:
An introduction
(or refresher) of
Statistical
Thermodynamics
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Outline
• Basic Assumption
– micro-canonical ensemble
– relation to thermodynamics
• Canonical ensemble
– free energy
– thermodynamic properties
• Other ensembles
– constant pressure
– grand-canonical ensemble
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Statistical Thermodynamics: the basics
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• Nature is quantum-mechanical
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• Consequence:
– Systems have discrete quantum states.
– For finite “closed” systems, the number of states is finite (but usually
very large)
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• Consequence:
very large)
• Hypothesis: In a closed system, every state is equally likely to be

observed.
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• Consequence:
very large)
• Hypothesis: In a closed system, every state is equally likely to be

observed.
• Consequence:
ALL of equilibrium Statistical Mechanics and Thermodynamics
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Simpler example: standard statistics
First: Simpler example (standard statistics)
Draw N balls from an infinite vessel that contains an equal
Draw of
number N red
ballsand
from an balls
blue infinite vessel that contains an
equal number of red and blue balls
! !
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1.0
0.8
0.6
0.4
0.2
0.2 0.4 0.6 0.8 1.0
NR/N
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1.0
0.8 N=10
0.6
0.4
0.2
0.2 0.4 0.6 0.8 1.0
NR/N
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1.0
N=100
0.8 N=10
0.6
0.4
0.2
0.2 0.4 0.6 0.8 1.0
NR/N
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N=1000
1.0
N=100
0.8 N=10
0.6
0.4
0.2
0.2 0.4 0.6 0.8 1.0
NR/N
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N=1000
N=10000
1.0
N=100
0.8 N=10
0.6
0.4
0.2
0.2 0.4 0.6 0.8 1.0
NR/N
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Molecular consequence of
basic assumption
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Molecular consequence of
Each individual
microstate is equally
probable basic assumption
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Molecular consequence
Each individual
of
…, but there are not many
microstates that give these
probable basic assumption extreme results
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Molecular consequence
Each individual
of
…, but there are not many
microstates that give these
probable basic assumption extreme results
If the number of particles

is large (>100) the
probability functions for
these states are sharply
peaked
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Does the basis assumption lead to something that is
consistent with classical thermodynamics?
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Systems 1 and 2 are weakly coupled
such that they can exchange energy.
What will be E1?
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What will be E1?
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What will be E1?
BA: each configuration is equally probable; but the number of states that
give an energy E1 is not (yet) known.
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What will be E1?
BA: each configuration is equally probable; but the number of states that
give an energy E1 is not (yet) known.
The most likely E1, is the E1 that maximizes Ω1(E1)x Ω2(E-E1)

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( )
⎛ ∂ ln Ω1 E1 ⎞ ( )
⎛ ∂ ln Ω2 E − E1 ⎞
+ ⎜ =0
⎜ ⎟ ⎟
⎝ ∂E1 ⎠ N ,V ⎝ ∂E1 ⎠ N
1 1 2 ,V2
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Energy is conserved!
dE1=-dE2
( )
⎛ ∂ ln Ω1 E1 ⎞ ( )
⎛ ∂ ln Ω2 E − E1 ⎞
+ ⎜ =0
⎜ ⎟ ⎟
⎝ ∂E1 ⎠ N ,V ⎝ ∂E1 ⎠ N
1 1 2 ,V2
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dE1=-dE2
( )
⎛ ∂ ln Ω1 E1 ⎞ ( )
⎛ ∂ ln Ω2 E − E1 ⎞
+ ⎜ =0
⎜ ⎟ ⎟
⎝ ∂E1 ⎠ N ,V ⎝ ∂E1 ⎠ N
1 1 2 ,V2
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dE1=-dE2
( )
⎛ ∂ ln Ω1 E1 ⎞ ( )
⎛ ∂ ln Ω2 E − E1 ⎞
+ ⎜ =0
⎜ ⎟ ⎟
⎝ ∂E1 ⎠ N ,V ⎝ ∂E1 ⎠ N
1 1 2 ,V2
This can be seen as an

equilibrium condition
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dE1=-dE2
( )
⎛ ∂ ln Ω1 E1 ⎞ (
⎛ ∂ ln Ω2 E − E1 ⎞
+ ⎜
) =0
⎜ ⎟ ⎟
⎝ ∂E1 ⎠ N ,V ⎝ ∂E1 ⎠ N
1 1 2 ,V2
This can be seen as an

equilibrium condition
Indeed this is the condition for thermal equilibrium:

“no spontaneous heat flow between 1 and 2”
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Normally, thermal equilibrium means: equal temperatures
Let us define:
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Let us define:
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Let us define:
Then, thermal equilibrium is equivalent to:
This suggests that β is a function of T.
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Relation to thermodynamics
Conjecture:
Almost right.
Good features:
– Extensivity
– Third law of thermodynamics comes for free
Bad feature:
– It assumes that entropy is dimensionless but (for unfortunate,
historical reasons, it is not…)
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Relation to thermodynamics
Conjecture:
Almost right.
Good features:
– Extensivity
– Third law of thermodynamics comes for free
Bad feature:
– It assumes that entropy is dimensionless but (for unfortunate,
historical reasons, it is not…)
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We have to live with the past, therefore
With kB= 1.380662 10-23 J/K
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With kB= 1.380662 10-23 J/K
In thermodynamics, the absolute (Kelvin) temperature scale

was defined such that
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With kB= 1.380662 10-23 J/K

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With kB= 1.380662 10-23 J/K

n
dE = TdS-pdV + ∑ µi dN i
i =1
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With kB= 1.380662 10-23 J/K

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With kB= 1.380662 10-23 J/K

But we found (defined):
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And this gives the “statistical” definition of temperature:
with
1
β=
kB T
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And this gives the “statistical” definition of temperature:
with
1
β=
kB T
In short:
Entropy and temperature are both related
to the fact that we can COUNT states.
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Number of configurations
35
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How large is Ω?
35
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How large is Ω?
For macroscopic systems, super-astronomically large.
35
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How large is Ω?
For instance, for a glass of water at room temperature:
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How large is Ω?
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How large is Ω?
Macroscopic deviations from the second law of thermodynamics are not

forbidden, but they are extremely unlikely.
35
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Deviation from the 2nd law?
What is the probability that 1 mole of argon gas spontaneously lowers it
entropy by 0.00000001% (=10-10) ?
standard molar entropy of argon : Sargon =307.2 J/K mol-1

slightly lower entropy Sargon,low =307.2 (1 - 10-10) J/K mol-1
probability of occurrence is
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entropy by 0.00000001% (=10-10) ?

� � � −8
�
Ωargon,low Sargon,low − Sargon −3.07 × 10 −1015
P ≈ = exp = exp ≈ 10
Ωargon kB 1.38 × 10−23
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entropy by 0.00000001% (=10-10) ?

� � � −8
�
Ωargon,low Sargon,low − Sargon −3.07 × 10 −1015
P ≈ = exp = exp ≈ 10
Ωargon kB 1.38 × 10−23
A mathematical relation : 10-1015 ≠ 0
A physical relation : 10-1015 = 0
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Canonical ensemble
Consider a small system that can exchange heat with a big reservoir
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Canonical ensemble
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Canonical ensemble 1/kBT
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Canonical ensemble
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Canonical ensemble
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Canonical ensemble
Hence, the probability to find Ei:
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Canonical ensemble
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Canonical ensemble
Partition�
function:
Hence, the probability to find Ei: Q= exp(−Ej /kB T )
j
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Canonical ensemble
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Canonical ensemble
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Canonical ensemble
Boltzmann distribution
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Canonical ensemble
“Low energies are more likely than high energies”

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Thermodynamics
What is the average energy of the system?
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Thermodynamics
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Thermodynamics
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Thermodynamics
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Thermodynamics
Compare:
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Thermodynamics
Thermo recall
What is the average energy ofequation
Fundamental the system?
Helmholtz Free energy:
Compare:
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Thermodynamics
Compare:
Hence:
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The classical limit
We have assume quantum mechanics (discrete states) but
we are interested in the classical limit
Particles are indistinguishable
N
“volume of phase space”
Why does planck constant appear?
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Appearance of Plank’s constant?
Easiest to look at translation partition function Qx of particle in 1D box
1 2 p2 p= momentum
"trans = mv = m=mass
2 2m
Postulate quantum mechanics: p=h/λ met h Planck’s constant
Particle is standing wave with length
!
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1 2 p2 p= momentum
2 2m
! 2
2L p 2 ( h / #) n 2h 2
"= "trans = = =
n 2m 2m 8mL2
! !
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1 2 p2 p= momentum
2 2m
! 2
2L p 2 ( h / #) n 2h 2
"= "trans = = =
n 2m 2m 8mL2
" " $ ! n2h2 '
Qx = # exp(!!"trans ) = # exp & ! 2 )
n=1 n=1 % 8mL (
! !
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1 2 p2 p= momentum
2 2m
! 2
2L p 2 ( h / #) n 2h 2
"= "trans = = =
n 2m 2m 8mL2
" $ ! n2h2 ' "
Qx = # exp(!!"trans ) = # exp & ! 2 )
n=1 n=1 % 8mL (
! !
" ! ! n 2 h 2 /(8mL2 ) L 2" m
Qx = # 1
dne =
h !
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1 2 p2 p= momentum
2 2m
! 2
2L p 2 ( h / #) n 2h 2
"= "trans = = =
n 2m 2m 8mL2
" $ ! n2h2 ' "
Qx = # exp(!!"trans ) = # exp & ! 2 )
n=1 n=1 % 8mL (
! !
" ! ! n 2 h 2 /(8mL2 ) L 2" m
Qx = # 1
dne =
h !
now compare
� � to classical integration without Planck’s constant
� �
2 2
p p 2πm
Qx = dpdr exp(−β + U (r)) = L dp exp(−β )=L
2m 2m β
factor of h is missing for each degree of freedom.
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The classical limit
N
Volume of phase space (particle in a box)
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The classical limit
N
Volume of phase space (particle in a box)
Integration over the momenta can be carried out for most systems:
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The classical limit
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The classical limit
Define de Broglie wavelength:
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The classical limit
Define de Broglie wavelength:
Partition function:
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Example: ideal gas
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Example: ideal gas
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Example: ideal gas
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Example: ideal gas
Free energy:
! N ln " 3 # N lnV + N ln N # N
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Example: ideal gas
Free energy:
! N ln " 3 # N lnV + N ln N # N
! F = N ( ln( !! 3 ) "1) with density ρ=N/V
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Example: ideal gas
Thermo recall
Helmholtz Free energy:
Free energy: Pressure
! N ln " 3 # N lnV + N ln N # N
(
! F = NEnergy:
ln( !! 3
) "1) with density ρ=N/V
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Example: ideal gas
Free energy:
! N ln " 3 # N lnV + N ln N # N
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Example: ideal gas
Free energy:
! N ln " 3 # N lnV + N ln N # N
Pressure:
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Example: ideal gas
Free energy:
! N ln " 3 # N lnV + N ln N # N
Pressure: Energy:
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Ideal gas (2)
⎛ ∂F ⎞
Chemical potential: µi = ⎜ ⎟
∂N
⎝ i ⎠ T ,V , N j
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Ideal gas (2)
⎛ ∂F ⎞
∂N
⎝ i ⎠ T ,V , N j
! F = N ( ln( !! ) "1)
3
with density ρ=N/V
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Ideal gas (2)
⎛ ∂F ⎞
∂N
⎝ i ⎠ T ,V , N j
! F = N ( ln( !! ) "1)
3
with density ρ=N/V
!µ = ln ! 3 + ln "
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Ideal gas (2)
⎛ ∂F ⎞
∂N
⎝ i ⎠ T ,V , N j
! F = N ( ln( !! ) "1)
3
with density ρ=N/V
!µ = ln ! 3 + ln "
IG 0
βµ = βµ + ln ρ
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Heat capacity from energy fluctuation
!! E $ ! ! E $ ! !" $
CV = # & = # & # &
" ! T %V ,N " !" %V ,N " ! T %
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!! E $ ! ! E $ ! !" $ 2
"! E %
CV = # & = # & # & kBT CV = ! $ '
" ! T %V ,N " !" %V ,N " ! T % # !" &V ,N
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!! E $ ! ! E $ ! !" $ 2
"! E %
CV = # & = # & # & kBT CV = ! $ '
" ! T %V ,N " !" %V ,N " ! T % # !" &V ,N
" E exp(!! E )
i i
i
E =
" exp(!! E ) i
i
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!! E $ ! ! E $ ! !" $ 2
"! E %
CV = # & = # & # & kBT CV = ! $ '
" ! T %V ,N " !" %V ,N " ! T % # !" &V ,N
!
" E exp(!" E )
i i
kBT 2CV =! i
!" " exp(!" E ) i
i
2
" E exp(!" Ei ) #% " Ei exp(!" Ei ) &(
i
2
= i !% i (
" exp(! " Ei ) % " exp(! " Ei ) (
i $ i '
2 2 2
= E ! E = (E ! E )
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!! E $ ! ! E $ ! !" $ 2
"! E %
CV = # & = # & # & kBT CV = ! $ '
" ! T %V ,N " !" %V ,N " ! T % # !" &V ,N
!
" E exp(!" E )
i i
kBT 2CV =! i
!" " exp(!" E ) i
i
2
" E exp(!" Ei ) #% " Ei exp(!" Ei ) &(
i
2
P(E) fluctuation in E
= i !% i ( grows as 1/√N
" exp(! " Ei ) % " exp(! " Ei ) (
i $ i '
2 2 2
= E ! E = (E ! E )
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!"
Computing the pressure
∂F
P =−
∂V
F = −kT ln Q
Introduce “scaled” coordinates:
Introduce scaled coordinates
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Computing the pressure
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Free energy derivative can be written as ensemble average!
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For pairwise additive forces:
Then
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i and j are dummy variable hence:
And we can write
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But as action equals reaction (Newton’s 3rd law):
And hence
Inserting this in our expression for the pressure, we get:
Where
This is known as the virial expression
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What
Whatdo youif do
to do youif cannot
you can’t
useuse
the the virial
virial expression?
expression?
This will be the case e.g. with discontinuous potentials.
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Summary:
micro-canonical ensemble (N,V,E)
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Summary:
Partition function:
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Summary:
Partition function:
Probability to find a particular configuration
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Summary:
Partition function:
Entropy
S = kB lnQN,V ,E
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Summary:
Canonical ensemble (N,V,T)
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Summary:
Partition function:
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Summary:
Partition function:
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Summary:
Partition function:
Free energy
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Ensemble averages
For properties that only depend on the configurational part
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Ensemble averages
Probability to find a configuration:
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Ensemble averages
1
P(!) = exp ["!U(!)]
Q
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Ensemble averages
1
P(!) = exp ["!U(!)]
Q
Ensemble average:
A = " d!A(!)P(!)
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Ergodicity theorem
suppose we have an ensemble average of a system defined by U(Γ) obtained by MC
Now suppose we have a NVT molecular dynamics trajectory for the same system
A time average over the trajectory is simply
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Ergodicity theorem
Ergodicity theorem states that for an ‘ergodic system’
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Ergodicity theorem
Ergodicity theorem states that for an ‘ergodic system’
MC and MD give the same averages

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Other ensembles?
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Other ensembles?
In the thermodynamic limit the thermodynamic properties are
independent of the ensemble: so buy a bigger computer …
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Other ensembles?
However, it is most of the times much better to think and to carefully

select an appropriate ensemble.
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Other ensembles?

For this it is important to know how to simulate in the various ensembles.
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Other ensembles?
In the thermodynamic limit the thermodynamic properties
Course on are
independent of the ensemble: so buy a bigger
MDcomputer
and MC in…
different ensembles
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Other ensembles?

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Other ensembles?

But for doing this we need to know the Statistical Thermodynamics

of the various ensembles.
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Constant pressure simulations:
N,P,T ensemble
Consider a small system that can exchange volume

and energy with a big reservoir
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N,P,T ensemble

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N,P,T ensemble
1/kBT p/kBT
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N,P,T ensemble
Thermo recall
1/kBT p/kBT
Fundamental equation
Hence
and
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N,P,T ensemble
1/kBT p/kBT
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N,P,T ensemble

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N,P,T ensemble

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N,P,T ensemble

Hence, the probability to find Ei,Vi:
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N,P,T ensemble

Hence, the probability to find Ei,Vi:
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N,P,T ensemble (2)
In the classical limit, the partition function becomes
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N,P,T ensemble (2)
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N,P,T ensemble (2)
The probability to find a particular configuration:
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N,P,T ensemble (2)
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Grand-canonical simulations:
µ,V,T ensemble
Consider a small system that can exchange particles

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µ,V,T ensemble

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µ,V,T ensemble
1/kBT
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µ,V,T ensemble
-µ/kBT
1/kBT
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µ,V,T ensemble
Thermo recall
-µ/kBT
1/kBT
Fundamental equation
Hence
and
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µ,V,T ensemble
-µ/kBT
1/kBT
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µ,V,T ensemble

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µ,V,T ensemble

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µ,V,T ensemble

Hence, the probability to find Ei,Ni:
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µ,V,T ensemble

Hence, the probability to find Ei,Ni:
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µ,V,T ensemble (2)
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µ,V,T ensemble (2)
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µ,V,T ensemble (2)
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Summary
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Summary
• Molecular simulation is firmly rooted in equilibrium statistical
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Summary
• Basis of statistical thermodynamics: configurations with same energy

are equally likely: microcanonical ensemble
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Summary

• At constant temperature Boltzmann distribution follows:

canonical ensemble
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Summary


canonical ensemble
• other ensembles are isobaric and grand canonical ensembles
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Summary


canonical ensemble
• MD and MC are two roads to the same equilibrium answer: ergodicity
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Summary


canonical ensemble
• MD also gives dynamical properties (viscosity, diffusion etc)
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Summary


canonical ensemble
• MD also gives dynamical properties (viscosity, diffusion etc)
• Rest of the week: MC and MD in depth.
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The end
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Introduction To World of MD Simulations

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Introduction To World of MD Simulations

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Understanding

“The rest is chemistry…”.

“The rest is chemistry…”.

This is a heavy burden the shoulders of “chemistry”:

“The rest is chemistry…”.

This is a heavy burden the shoulders of “chemistry”:

The “rest” amounts to the quantitative description of the world around us

for a given intermolecular potential

for a given intermolecular potential

for a given intermolecular potential

for a given intermolecular potential

for a given intermolecular potential

for a given intermolecular potential

LAPLACE says: in principle yes,

LAPLACE says: in principle yes,

BOLZMANN says: yes, just solve my phase space integral

LAPLACE says: in principle yes,

BOLZMANN says: yes, just solve my phase space integral

both approaches should lead to the same results:

LAPLACE says: in principle yes,

BOLZMANN says: yes, just solve my phase space integral

1. Smart tricks (“theory”)

1. Smart tricks (“theory”)

2. Constructing a model (“molecular lego”).

J.D. Bernal’s ball-bearing model Watson and Crick’s model of

With computers we can follow the behavior of hundreds to

100 Tflop/s 56/%

To predict the thermodynamic properties (boiling points)

United-atom model CH2 CH2

• Transition path sampling

• Transition path sampling

• Transition path sampling

• Transition path sampling

• Transition path sampling

Leads to insight and

• Bernie Alder et al. carried out

• Bernie Alder et al. carried out

• Bernie Alder et al. carried out

• Bernie Alder et al. carried out

from :Yethiraj and van Blaaderen

and show that hard spheres indeed crystallize at high density

• Coarse-grained model of a membrane to study the interactions

• Coarse-grained model of a membrane to study the interactions

• Coarse-grained model of a membrane to study the interactions

• Coarse-grained model of a membrane to study the interactions

• Make simple lattice model with

• Make simple lattice model with

• Make simple lattice model with

• MC simulation yields understanding

• Make simple lattice model with

• MC simulation yields understanding

• Need different levels of

• Result: “Experulation” or “Simuriment”.

• Result: “Experulation” or “Simuriment”.

• Simulations are becoming an integral part of the analysis of experimental

• Hypothesis: In a closed system, every state is equally likely to be

• Hypothesis: In a closed system, every state is equally likely to be

0.2 0.4 0.6 0.8 1.0

0.2 0.4 0.6 0.8 1.0

0.2 0.4 0.6 0.8 1.0

0.2 0.4 0.6 0.8 1.0

0.2 0.4 0.6 0.8 1.0