Molecular Dynamics Flashcards
Define System, Model and Simulation
a) SYSTEM is a part of the “universe” or set of variables and environment that we would like to study
b) MODEL is a simplified representation of our system
c) SIMULATION is a numerical or computer-based calculation of our system
What constitutes a good model?
- Fast
- Accurate
- Time reversible
Since Newton’s eqn of motion is time reversible
Describe the basic algorithm of MD
- Initialization -Read OFF the pre-set variables such as:
initial position, velocity (MB distribution).. Temperature etc.
boundary condition, pair potential… - Calculate Force -Integration of Newton’s equation of motion F=ma
- Move particles and update time - Integrators [e. g. varlet or leapfrog] and wait until equilibrium is reached
- Output the data: Observables (Temp, Pressure, Energy, )
How is MD initialized?
- MD is initialized by setting up the position and velocity of a particle
- Position can be initialized by placing the particles in lattice sites
- Velocity can be initialized by using Maxwell-Boltzmann distribution
Write down and Explain Maxwell-Boltzmann Distribution
- MB distribution is a probability distribution of a particles’ most probable speed given at a specific temperature.
- Simulation will take a random value From 0 to 1 at T thus we can get the velocity
What are boundary conditions?
Boundary conditions are parameters or limits that can make calculation of force faster, some examples are;
- critical radius
- hard sphere
- periodic box
What is cut off radius?
- Cut of radius is the inter atomic distance when the force is at minimum
- It is also equivalent to 1.12* Van der Waals radius
- Represents the cut off potential, anything greater than rc is neglected
- rc is used as one method to reduce computational cost
What are dimensionless units?
Because computer only know numbers, dimensionless units are derived from basic parameters which prevents large numeric values from different units
How to choose the best time step?
- Choose largest time step as possible (stable] to speed up simulation
- The value should be proportional to the particle vibration (up to 100 times larger)
- For atomic simulations ~10^14 seconds, thus can set 10^15 seconds
Briefly define molecular dynamics
Molecular Dynamics is a computer simulation method that analyzed the time evolution of atomic interactions by numerical integration of Newton’s equation of motion