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Lecture 1
Lecture 1
Michael P Allen
G L S
T
t
P
Simple phase diagram: gas–liquid–solid
G L S
T
t
P
Simple phase diagram: gas–liquid–solid
G L S
T
t
P
Simple phase diagram: gas–liquid–solid
G L S
T
t
P
Simple phase diagram: gas–liquid–solid
G L S
T
t
ρ
Simple phase diagram: gas–liquid–solid
G L S
T
t
ρ
Molecular simulation
What is it?
100
101
102
103
104
105
106
19
50
Growth of the field
–5
9
19
60
–6
9
19
70
–7
9
19
80
–8
Decade
9
19
90
–9
9
20
00
–0
9
Molecular simulation
Bridging experiment and theory
Compare Compare
Compare Compare
I Simulation box is
cubic.
I Surround cube with
1 4 replicas.
2
3
I If a molecule leaves
5 the basic simulation
box, attention can
be switched to the
incoming image.
L
Periodic Boundary Conditions
For short-range
potentials, adopt the
minimum image
1 convention: each atom
4
interacts with the
2
nearest atom or image in
5 3
the periodic array.
No more interfaces;
however the periodicity
is artificial!
Angular momentum
pi
X
L= ri × p i
fj i
X
i L̇ = ri × fi
j
i
100
−100
actual pair potential
3
σ 12 σ 6
2 vLJ (r) = 4ε −
r r
v(r)/ε
1 (12)
vLJ (12) (6)
vLJ = vLJ (r) + vLJ (r)
0
σ = diameter
−1
ε = well depth
(6)
vLJ
−2
0.8 1.0 1.2 1.4 1.6 1.8 2.0
r/σ
Lennard-Jones potential
rij dv(rij )
fi = −fj = −∇i v(rij ) = −
rij drij
σ 12 σ 6
vLJ (r) = 4ε −
r r
σ 6
r dvLJ (r) 4ε σ 12
fLJ (r) = − = 2 12 −6 r
r dr r r r
4
3
Alternative division into
attractive and repulsive parts:
2
v(R)
v(r)/ε
LJ
1
vLJ
vLJ (r) = v(R) (A)
LJ (r) + vLJ (r)
0
r 6 rmin r > rmin
−1
v(A)
v(R)
LJ (r) = vLJ (r) + ε 0
LJ
−2
0.8 1.0 1.2 1.4 1.6 1.8 2.0 v(A)
LJ (r) = −ε vLJ (r)
r/σ
Three-body forces
Triple-dipole interaction
rj
θj rjk
rij
θi θk
ri rk
rki
i
j
a=1
b=2
a=2
b=1
Linear molecule forces and torques
ei
θi
ej
φij
θj ri
rij
rj
Rigid molecular interactions
JG Gay, BJ Berne, J Chem Phys, 74, 3316 (1981).
4.0
2.0
v(r)/0
0.0
−2.0
−4.0
H H
+q +q
−2q
q2 (t) q1 (t)
O
q4 (t)
q3 (t)
ra−2
ra−4 θa−1
φa−1
ra−1 ra+1
da−3 da−1 φ
a
da−2
θa−2 θa φ
da a+1
ra−3 da+1
θa+1
ra
200
150
v(r)/
100
50
0
0.0 0.5 1.0 1.5
r/σ
Angle torsion potential
2 000
1 000
500
0 π
−π 0
φ (radians)
Deriving forces from potentials
σ σ1
σ2
r r
Outline
Introduction
Statistical mechanics
Molecular dynamics
Monte Carlo methods
Some tricks of the trade
Long-range forces
Parallel Simulation
How to analyse the results
Advanced Monte Carlo methods
Rare-event simulation
Non-equilibrium molecular dynamics
Mesoscale methods
Quantum simulations
Inhomogeneous fluids
Simulation and statistical mechanics