Lecture 4: Atomistic Models

Question 1

What are atoms represented in atomistic simulations?

Answer 1

Beads

Question 2

What are the length and time scales of atomistic simulations?

Answer 2

Length scale= nm
Timescale = nanoseconds

Question 3

What does each bead have?

Answer 3

Specific parameters e.g. radius, interaction, charge

Question 4

How are beads arranged to make molecules?

Answer 4

Beads are joined with springs

Question 5

What is the energy of the force field made from?

Answer 5

Sum of non-bonded energy, bond stretching, bending energy, rotation around a bond, improper inversions, charges, cross-terms

Question 6

What are non-bonded parameters? (E nonbond)

Answer 6

-Van der Waals forces between all beads
-specific to each element type and chemical environment
-pair wide potential
-common functional forms: LJ potential, Morse potential

Question 7

Describe the Lennard-Jones potential

Answer 7

-as two particles get closer, prob of them interacting increases
-when two particles get closer and they become bound their bonding potential energy becomes negative
-while the particles are bound, the distance between particles decreases until an equilibrium is formed and minimum potential energy reached
-if two bound particles are pushed beyond equilibrium they repel each other and energy increases rapidly

Question 8

What are mixing rules?

Answer 8

-Calculations that determine how atoms interact with each other
-can calculate interaction potentials

Question 9

Which is more computationally expensive? LJ or Buckingham potential?

Answer 9

Buckingham potential

Question 10

How does the Buckingham potential arise?

Answer 10

The repulsion (exponential) is caused by the interpénétration of closed shell electrons

Question 11

At small radii, how does the energy of the LJ potential and Buckingham potentials compare?

Answer 11

LJ -> infinity as they repel
Buck -> 0 which is unphysical

Question 12

What is the Morse potential in the bonded parameters? (Bond stretching)

Answer 12

-The quantum harmonic oscillator
-How the energy changes as molecules oscillate

Question 13

What happens in the bonding energy at large radii in the Morse model

Answer 13

There is low energy, so can be slow to equilibrate

Question 14

In the harmonic oscillator model, what is the best radii distance for a harmonic bond?

Answer 14

When E=0

Question 15

Which is more commonly used? Morse or harmonic oscillator?

Answer 15

Harmonic oscillator model

Question 16

In the Morse potential, what does D , alpha, and r stand for?

Answer 16

D= dissociation energy
Alpha= sqrt(k/2D)
r=equilibrium length

Question 17

In harmonic oscillator, what does k stand for? What does r stand for?

Answer 17

k= Bond strength/spring constant
r=equilibrium length

Question 18

What is E angle? (Bonding energy for 3 atoms)

Answer 18

-also uses harmonic potential
-usually smaller than bonded

Question 19

In the angle harmonic potentialC what does theta and k stand for?

Answer 19

k= spring constant/angle strength
Theta=equilibrium angle

Question 20

How are dihedral or torsional potentials created?

Answer 20

By four linearly aligned atoms

Question 21

How many dihedral angles are there in ethane?

Answer 21

6

Question 22

In dihedral parameters, how can rotation be described?

Answer 22

Rotation is continuous and periodic

Question 23

In the Fourier transform of dihedral angle potential, what does Vn, phi and n stand for?

Answer 23

Vn=barrier to rotation constant
n=periodicity
Phi=equilibrium dihedral angle

Question 24

What are improper parameters used for?

Answer 24

Used to penalise out of plane bending
Often uses harmonic equation

Question 25

What are the charges (E coulomb) treated as?

Answer 25

-treated as point charges
-simplest
-unlike other contributions, charges are long range
-decay as 1/r

Question 26

What are cross terms? (E xterm)

Answer 26

Couple different motions together e.g. fundamental bond stretching and bending

Question 27

How do we choose a force field?

Answer 27

1. Does it include all the species we need in our system?
2. What experimental property was it parameter used against and what do we want to use it for?
3. If we need to use two force fields, are they compatible?

Question 28

What is annoying about water?

Answer 28

It’s everywhere but we can’t capture all the properties in one model

Question 29

Describe a 3-site water model

Answer 29

• 6 parameters: 2 non-bonded (O, H), 2 charges (qH, qO), 1 bond, 1 angle
  -common approximations: fixed bond lengths and angles, H non-bonded interactions often zero

Question 30

What are examples of 3-site water models?

Answer 30

SPC, TIP3P, SPC/E

Question 31

Describe a 4 site water model

Answer 31

• 9 parameters: 2 non-bonded (O, H), 3 charges (qH, qO, qD), 2 bonds (b1,b2), 2 angles (between hydrogens, and between hydrogen and dummy)

Question 32

What does a dummy charge do in 4-site water models?

Answer 32

Improves electrostatic distribution
Dummy can be in two places

Question 33

What are examples of 4-site water molecule?

Answer 33

TIP4P, TIP4P-Ew, TIP4P/2005, COS/D, SWFLEX-AI

Question 34

Describe a 4+-site water model

Answer 34

-5 site in tetrahedral arrangement
-two dummy charges
-many body potentials, not based on pairwise potentials

Question 35

What are polarisable water models?

Answer 35

They capture quantum effects but are more expensive

Question 36

What are one-site water models?

Answer 36

-coarse-graining where water is represented as single bead
-SSD (soft sticky dipole) tetrahedral coordinated sticky potential that regulated tetrahedral coordination to neighbouring sites

Question 37

What are implicit water models?

Answer 37

-General effects of water are taken into account but the molecules are not directly simulated
-can greatly reduce computational cost