Molecular Dynamics

Question 1

What is Molecular Dynamics

Answer 1

Using classical methods to analyse the positions and velocities of atoms in a system at specific time points to produce a trajectory
Based on Newtons Law of Motion F=ma where F is the negative gradient of the potential energy

Question 2

Formula of Kinetic Energy

Answer 2

1/2 mv^2 = 3/2 NKBT

Question 3

Given a high/ low temperature, how does this affect a MD simulation

Answer 3

High temp -> higher average velocities -> cross PE barrier more often -> require shorter time steps

Low temp -> lower average velocities -> motion trapped around PE minima -> time steps don’t have to be as short

Question 4

Define:
Local Minima
Global minima

Answer 4

Local minima - the lowest point in a given section
Global minima - the lowest point overall (most stable structure overall)

Question 5

Total Energy of a system E(t)=

Answer 5

PE(t) + KE(t)
potential + kinetic

Question 6

What is a timestep?
What is atomic motion to the order of?

Answer 6

Timestep -
In MDs positions and velocities are computed at specific points in time (not continuous but at quantised steps) where the delay between their positions and velocities is the timestep Δt
atomic motion time step order: 1 fs (10^-15s)

Question 7

Define:
- Configuration
- Ensamble
- Trajectory

Answer 7

• configuration
  the specific arrangement (position and velocity) of atoms in the system at a specific time point
• trajectory
  a time-ordered collection of positions and velocities of atoms to depict the motion during a simulation
• ensamble
  a collection of configurations ran under the same conditions (not necessarily time ordered)

Question 8

What is the limitation of MDs?

Answer 8

Time scales
Long simulations require rapid evaluation of atomic forces (expensive over a long time) and so typically use empirical forcefields making molecular mechanics more suitable for this

Question 9

What is an ensemble average?

Answer 9

The average value of a physical quantity calculated over a large number of molecular configurations sampled from an ensamble
provides insight into the behaviour and properties of the system under certain conditions

Question 10

What are 4 common simulation conditions?

Answer 10

1. Microcanonical ensemble NVE
2. Canonical ensemble
   NVT
3. isothermal-isobaric NPT
   4.grand-canonical ensemble μVT

Question 11

What are the 3 common conformational search methods?

Answer 11

1. Systematic grid search
   finding the most stable conformer by finding all minima by systematic search go structural parameters (then optimise to minima)
2. Monte Carlo
   Guessing a starting structure and defining co-ordinates (usually τ)to be varied and apply random variations, energy optimise then compare to other minima
3. Simulated annealing
   guess a starting structure and perform a high temp MD simulation got a short period to change the conformation, stop the simulation, energy optimise and compare to other minima

Question 12

What do trajectories provide insight into?

Answer 12

-structural changes
-dynamics of motion (vibration, motion, rotation etc.)
-interactions
-thermodynamics
-validation - making sure simulation lines up with other experimental and theoretical data and models