YuShan Lin YSL Department of Chemistry Tufts University Simulate how molecules move Molecular dynamics simulations km hr v 0 100 1000 kg 7000 N m s 2 ID: 528010
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Slide1
Intro to molecular dynamics simulation
Yu-Shan Lin (YSL)
Department of
Chemistry
Tufts
UniversitySlide2
Simulate how molecules move
Molecular dynamics simulations
km
hr
v
(0)
=
=
100
= 1000 kg
=
−
7000 N
m
s2
m
F
a
m
s
=
28
=
v
(t)
= v(0)+at = 28−7t
=
x (t)
= 28t − t 2
=
7
2
x
(0)
= 0 m
m
=
−7
F
=
0
t
v
(
t’ )dt’
200
ft
= 61 m
Can predict the position and speed of the car at any time.Slide3
km
hr
v
(0)
=
=
100
= 1000 kg
=
−7000 N
m
s2
m
F
a
m
s
=
28
=
v
(t)
= v(0)
+at = 28−7t
=
x (t)= 28t
− t 2
=
72
x
(0)
= 0 m
m
=
−7
F
=
0
t
v
(
t’ )dt’
v
(1s)
= 21
x (1s)
= 24.5 m
ms
Simulate how molecules move
Molecular dynamics simulations
200
ft
=
61
m
Can predict the position and speed of the car at any time.Slide4
km
hr
v
(0)
=
=
100
= 1000 kg
=
−7000 N
m
s2
m
F
a
m
s
=
28
=
v
(t)
= v(0)
+at = 28−7t
=
x (t)= 28t
− t 2
=
72
x
(0)
m
=
−7
F
=
0
t
v
(t’
)dt’
v (2s)
= 14
x
(2s)
= 42 m
m
s
Simulate how molecules move
= 0 m
Molecular dynamics simulations
200
ft
=
61
m
Can predict the position and speed of the car at any time.Slide5
km
hr
v
(0)
=
=
100
= 1000 kg
=
−7000 N
m
s2
m
F
a
m
s
=
28
=
v
(t)
= v(0)
+at = 28−7t
=
x (t)= 28t
− t 2
=
72
x
(0)
m
=
−7
F
=
0
t
v(
t’ )dt’
v
(3s)
= 7
x (3s)
= 52.5 m
m
s
Simulate how molecules move
= 0 m
Molecular dynamics simulations
200
ft
=
61
m
Can predict the position and speed of the car at any time.Slide6
km
hr
v
(0)
=
=
100
= 1000 kg
=
−7000 N
m
s2
m
F
a
m
s
=
28
=
v
(t)
= v(0)
+at = 28−7t
=
x (t)= 28t
− t 2
=
72
x
(0)
m
=
−7
F
=
0
t
v(
t’ )dt’v
(4s)
= 0
x (4s)
= 56 m
m
s
Simulate how molecules move
= 0 m
Molecular dynamics simulations
200
ft
=
61
m
Can predict the position and speed of the car at any time.Slide7
km
hr
v
(0)
=
=
100
= 1000 kg
=
−7000 N
m
s2
m
F
a
m
s
=
28
=
v (t)
= v(0)
+at = 28−7t
=
x (t)
= 28t − t 2
=
7
2x
(0)
= 0 m
m
=
−7
F
=
0
t
v(
t’ )dt’
Simulate how molecules move
Molecular dynamics simulations
Can predict the position and speed of the car at any time.Slide8
km
hr
v
(0)
=
=
100
= 1000 kg
=
−7000 N
m
s2
m
F
a
m
s
=
28
=
v (t)
= v(0)
+at = 28−7t
=
x (t)
= 28t − t 2
=
7
2x
(0)
= 0 m
m
=
−7
F
=
0
t
v(
t’ )dt’
Simulate how molecules move
This is a car
Na
+
Cl
-
Cl
-
x
2
(0),
v
2
(0)
x
3
(0),
v
3
(0)
x
1
(0),
v
1
(0)
Your system looks more like this…
Molecular dynamics simulations
Can predict the position and speed of the car at any time.Slide9
km
hr
v
(0)
=
=
100
= 1000 kg
=
−7000 N
m
s2
m
F
a
m
s
=
28
=
v (t)
= v(0)
+at = 28−7t
=
x (t)
= 28t − t 2
=
7
2x
(0)
= 0 m
m
=
−7
F
=
0
t
v(
t’ )dt’
Na+
Cl
-
Cl-
F
1 (0)
x
2
(0),
v
2
(0)
F
2
(0)
F
3
(0)
x
3
(0),
v
3
(0)
x
1
(0),
v
1
(0)
Simulate how molecules move
This is a car
Your system looks more like this…
Molecular dynamics simulations
Can predict the position and speed of the car at any time.Slide10
km
hr
v
(0)
=
=
100
= 1000 kg
=
−7000 N
m
s2
m
F
a
m
s
=
28
=
v (t)
= v(0)
+at = 28−7t
=
x (t)
= 28t − t 2
=
7
2x
(0)
= 0 m
m
=
−7
F
=
0
t
v(
t’ )dt’
Na+
Cl
-
Cl-
x2(dt), v2(d
t)
x3(dt), v3(dt)
x1(dt
),
v
1
(d
t
)
Simulate how molecules move
This is a car
Your system looks more like this…
Molecular dynamics simulations
Can predict the position and speed of the car at any time.Slide11
km
hr
v
(0)
=
=
100
= 1000 kg
=
−7000 N
m
s2
m
F
a
m
s
=
28
=
v (t)
= v(0)
+at = 28−7t
=
x (t)
= 28t − t 2
=
7
2x
(0)
= 0 m
m
=
−7
F
=
0
t
v(
t’ )dt’
Na+
Cl
-
Cl-
x2(dt), v2(d
t)
x3(dt), v3(dt)
x1(dt
),
v
1
(d
t
)
F
1
(d
t
)
F
2
(d
t
)
F
3
(d
t
)
Simulate how molecules move
This is a car
Your system looks more like this…
Molecular dynamics simulations
Can predict the position and speed of the car at any time.Slide12
km
hr
v
(0)
=
=
100
= 1000 kg
=
−7000 N
m
s2
m
F
a
m
s
=
28
=
v (t)
= v(0)
+at = 28−7t
=
x (t)
= 28t − t 2
=
7
2x
(0)
= 0 m
m
=
−7
F
=
0
t
v(
t’ )dt’
Na+
Cl
-
Cl-
x2(dt), v2(d
t)
x3(dt), v3(dt)
x1(dt
),
v
1
(d
t
)
F
1
(d
t
)
F
2
(d
t
)
F
3
(d
t
)
Simulate how molecules move
This is a car
Your system looks more like this…
Molecular dynamics simulations
Can predict the position and speed of the car at any time.Slide13
km
hr
v
(0)
=
=
100
= 1000 kg
=
−7000 N
m
s2
m
F
a
m
s
=
28
=
v (t)
= v(0)
+at = 28−7t
=
x (t)
= 28t − t 2
=
7
2x
(0)
= 0 m
m
=
−7
F
=
0
t
v(
t’ )dt’
Na+
Cl
-
Cl-
x2(2*dt), v2(2*d
t)
x3(2*dt), v3(2*dt)
x1(2*d
t
),
v
1
(2*d
t
)
Simulate how molecules move
This is a car
Your system looks more like this…
Molecular dynamics simulations
Can predict the position and speed of the car at any time.Slide14
Non-bonded
Van der Waals interaction
Bond stretch
Angle bending
Torsion
Non-bonded
electrostatic interaction
−
+
Simulate how molecules move
These parameters form a “force field”
Molecular dynamics simulationsSlide15
Different “force fields” have different flavors…
“
spc
/e”
“
tip3p
”
s
imple
point charge/extended
t
ransferable intermolecular potential 3-p
ointExample: There are many water models…
D25
°C (10-5 cm2/s)
2.5
5.5
Exp
: 2.3
+0.4238
−0.8476
+0.4170
−0.8340
+0.4170
+0.4238
1.0000
Å
0.9572 Å
109.47°104.52°Example: There are many peptide force fields…
“Helix-friendly”
“β-Sheet-friendly”
Molecular dynamics simulations
Diffusion coefficient at
25°CSlide16
Non-bonded
Van der Waals interaction
Bond stretch
Angle bending
Torsion
Non-bonded
electrostatic interaction
−
+
Simulate how molecules move
These parameters form a “force field”
Molecular dynamics simulationsSlide17
Protein folding simulation of NTL9
N-terminus
C-terminus
β
1
β
2
β
3
α
1.5µs of simulation = [ 600x10
6
steps ]x[ 2.5fs/step ]
Movie: configuration at every 1ns, 1500 snapshots
K. Lindorff-Larsen, S. Piana, R. O. Dror, D. E. Shaw,
Science
334
, 517 (2011)
“Primary sequence”
α
-Helix
3
10
-Helix
β
-sheet
β
-bridge
M
K
VIFL
K
D
V
K
GMG
KK
G
E
I
K
N
VA
D
G
Y
A
NN
FLF
K
QG
LAI
E
A
TP
A
N
L
K
AL
E
A
Q
K
Q
+
+
-
+ ++
-
+
-
+
-
+
-
+Slide18
Argon atoms
Molecular dynamics s
imulations
Goal: (what do you want to do?)
To study the structure and dynamics of Ar
You meant…?
Temperature=?
Volume/
Pressure=?
Phase diagram of Ar
Ar liquid/gas interface?
A droplet of Ar?
Liquid Ar?
3 Ar atoms? Slide19
Argon atoms
Molecular dynamics s
imulations
Method: (how are you going to do it?)
Classical molecular dynamics simulations
Is this a suitable method? Are there situations where classical molecular dynamics simulations won’t work?
MD simulations of liquid
Periodic Boundary
ConditionSlide20
Argon atoms
Molecular dynamics s
imulations
Method: (how are you going to do it?)
Classical molecular dynamics simulations
Is this a suitable method? Are there situations where classical molecular dynamics simulations won’t work?
MD simulations of liquid
Periodic Boundary
Condition
Minimum-Image ConventionSlide21
Three basic ingredients
Molecular dynamics s
imulations
Now what do you need?
1. Description of initial positions
1
.
Description of initial velocities
2
.
Description of interaction potentials (aka “force field”)
Maxwell-Boltzmann
Distribution
Equipartition Theorem
3. An integrator
Leap-frog Algorithm
Lennard-Jones Potential
/Force (and others)
Cut-off? Hard/Shifted/Shift-forceSlide22
Molecular dynamics
simulationsTo learn more about running MD simulations, visit our website at
http://
ase.tufts.edu
/chemistry/
lin
/outreach.html