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Module-3: Ab Initio Molecular Dynamics

This document provides an overview of ab initio molecular dynamics simulations. It discusses how molecular dynamics simulations integrate the classical equations of motion to simulate atomic motion over time using numerical integration methods like the velocity Verlet algorithm. Forces are derived from the potential energy surface, such as the Lennard-Jones potential for interatomic interactions. Ab initio molecular dynamics specifically uses quantum mechanical calculations to determine the potential energy and atomic forces at each time step. An example of simulating a 1D harmonic oscillator analytically and a 2D harmonic oscillator is presented to illustrate the methodology.

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Anubhav Vardhan
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86 views22 pages

Module-3: Ab Initio Molecular Dynamics

This document provides an overview of ab initio molecular dynamics simulations. It discusses how molecular dynamics simulations integrate the classical equations of motion to simulate atomic motion over time using numerical integration methods like the velocity Verlet algorithm. Forces are derived from the potential energy surface, such as the Lennard-Jones potential for interatomic interactions. Ab initio molecular dynamics specifically uses quantum mechanical calculations to determine the potential energy and atomic forces at each time step. An example of simulating a 1D harmonic oscillator analytically and a 2D harmonic oscillator is presented to illustrate the methodology.

Uploaded by

Anubhav Vardhan
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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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

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