Module-3

Ab Initio Molecular
Dynamics
March 18

PLAN

Molecular Dynamics (MD)

Simulation
Ab initio MD

R. Car and M. Parrinello Phys. Rev. Lett. 55, 2471, 1985

Molecular Dynamics

We like to move....atoms!

How can I do it?

The Story of Newtons Apple...

Equations of motion:
d2 x
F =m 2
dt

Solving (integrating) D.E.

We may use numerical or analytical
integration

Mangalyaan Mission

trusting
truly on the
classical
equations of
motion

F=ma

also used to create your favorite characters!

how to get forces?

Born-Oppenheimer Molecular Dynamics

@U (x1 , x2 , , xn )
@xi

Fi =

gradient

Ab Initio Molecular Dynamics

N

U (R ) = min
{ i}

el

|H |

+ ENN

Demonstration:
1D-Harmonic Oscillator
1 2
U (x) = kx
2
F =
=

dU
dx
kx

d x
)m 2 =
dt

kx

Analytical solution obtainable

Req. two initial conditions:

x(0)

&

x(0)

 Analytical integration of differential

equation:

For the initial conditions: x(0) = A v(0) = 0

x(t) = A cos(!t)
!=

v(t) =

k
m

Aw sin(!t)

time(t)

x(t); v(t)

2D-Harmonic Oscillator
1 2 1 2
U (x, y) = kx + ky
2
2

U(x,y)

Fx =

@U
=
@x

kx

Fy =

@U
=
@y

ky

F = F x i + Fy j

U(x,y)

forces direct the system to the minimum PE

PE
KE

How about atoms?

Classical mechanics? or quantum mechanics?
It is a good assumption to treat the atomic
motions classically

d2 xi
Fi = mi 2
dt
atom 1

v1

v3

atom 3
atom 2

v2

i=1,3N
N=number of particles

each degree of
freedom of an
atom will be
having unique
positions,
velocities, and
forces

 Each degree of freedom has an equation of

motion (classical) as you have seen for a
2D-harmonic oscillator (before)

For e.g. consider two atoms:

Fx 1
Fy 1
Fz 1

For atom 2

For atom 1
d x1
= M1 2
dt
d 2 y1
= M1 2
dt
d 2 z1
= M1 2
dt

Fx 2
Fy 2
Fz 2

d2 x2
= M2 2
dt
d 2 y2
= M2 2
dt
d 2 z2
= M2 2
dt

z2

z1

x1

y1
x2

6 Eq. of
motion to
solve
independently

y2

 The force acting on each degree of

freedom of every atom has the information

about the inter-atomic interactions

Interatomic interactions are governed by

the potential energy surface (as negative of

the gradient of the potential energy is the
force)

Lennard Jones Potential

LJ potential is an example of interatomic interaction
ULJ (R1 , , RN ) =

XX
I

J>I

RIJ = |RI

"

RIJ

12

RIJ

6 #

RJ |

FI =

@ULJ (R1 , , RN )
@RI
I = 1, , N

Note: it is a 3D-vector
(x,y,z components)

Numerical Integration
VI (t) = VI (0) +

RI (t) = RI (0) +

t
0

FI ( )
d
MI

atom 1

d VI ( )

atom 2

many body
interactions within the
force: numerical
integration is required

atom 3

R
t

Velocity Verlet Algorithm

Originally by Carl Stoermer (in 1907, particles in electric field)

RI (t +

1
I (t) t + R
I (t) t2 + O( t3 )
t) = RI (t) + R
2
e
v
i
at

v
i
r
de

ULJ (R1 (t), , RN (t))

ve
ati
riv
de

I (t +
R

I (t) +
t) = R

h
t

t), , RN (t +

deriv
ative

ULJ (R1 (t +

I (t) + R
I (t +
R

t))

t) + O( t )

Molecular Dynamics (MD)

R I

RI

velocity Verlet

I (0)
RI (0), R

I ( t)
RI ( t), R

trajectory

I (2 t)
RI (2 t), R