Lecture 4: Atomistic Models Flashcards
What are atoms represented in atomistic simulations?
Beads
What are the length and time scales of atomistic simulations?
Length scale= nm
Timescale = nanoseconds
What does each bead have?
Specific parameters e.g. radius, interaction, charge
How are beads arranged to make molecules?
Beads are joined with springs
What is the energy of the force field made from?
Sum of non-bonded energy, bond stretching, bending energy, rotation around a bond, improper inversions, charges, cross-terms
What are non-bonded parameters? (E nonbond)
-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
Describe the Lennard-Jones potential
-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
What are mixing rules?
-Calculations that determine how atoms interact with each other
-can calculate interaction potentials
Which is more computationally expensive? LJ or Buckingham potential?
Buckingham potential
How does the Buckingham potential arise?
The repulsion (exponential) is caused by the interpénétration of closed shell electrons
At small radii, how does the energy of the LJ potential and Buckingham potentials compare?
LJ -> infinity as they repel
Buck -> 0 which is unphysical
What is the Morse potential in the bonded parameters? (Bond stretching)
-The quantum harmonic oscillator
-How the energy changes as molecules oscillate
What happens in the bonding energy at large radii in the Morse model
There is low energy, so can be slow to equilibrate
In the harmonic oscillator model, what is the best radii distance for a harmonic bond?
When E=0
Which is more commonly used? Morse or harmonic oscillator?
Harmonic oscillator model
In the Morse potential, what does D , alpha, and r stand for?
D= dissociation energy
Alpha= sqrt(k/2D)
r=equilibrium length
In harmonic oscillator, what does k stand for? What does r stand for?
k= Bond strength/spring constant
r=equilibrium length
What is E angle? (Bonding energy for 3 atoms)
-also uses harmonic potential
-usually smaller than bonded
In the angle harmonic potentialC what does theta and k stand for?
k= spring constant/angle strength
Theta=equilibrium angle
How are dihedral or torsional potentials created?
By four linearly aligned atoms
How many dihedral angles are there in ethane?
6
In dihedral parameters, how can rotation be described?
Rotation is continuous and periodic
In the Fourier transform of dihedral angle potential, what does Vn, phi and n stand for?
Vn=barrier to rotation constant
n=periodicity
Phi=equilibrium dihedral angle
What are improper parameters used for?
Used to penalise out of plane bending
Often uses harmonic equation
What are the charges (E coulomb) treated as?
-treated as point charges
-simplest
-unlike other contributions, charges are long range
-decay as 1/r
What are cross terms? (E xterm)
Couple different motions together e.g. fundamental bond stretching and bending
How do we choose a force field?
- Does it include all the species we need in our system?
- What experimental property was it parameter used against and what do we want to use it for?
- If we need to use two force fields, are they compatible?
What is annoying about water?
It’s everywhere but we can’t capture all the properties in one model
Describe a 3-site water model
- 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
What are examples of 3-site water models?
SPC, TIP3P, SPC/E
Describe a 4 site water model
- 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)
What does a dummy charge do in 4-site water models?
Improves electrostatic distribution
Dummy can be in two places
What are examples of 4-site water molecule?
TIP4P, TIP4P-Ew, TIP4P/2005, COS/D, SWFLEX-AI
Describe a 4+-site water model
-5 site in tetrahedral arrangement
-two dummy charges
-many body potentials, not based on pairwise potentials
What are polarisable water models?
They capture quantum effects but are more expensive
What are one-site water models?
-coarse-graining where water is represented as single bead
-SSD (soft sticky dipole) tetrahedral coordinated sticky potential that regulated tetrahedral coordination to neighbouring sites
What are implicit water models?
-General effects of water are taken into account but the molecules are not directly simulated
-can greatly reduce computational cost
