Molecular Dynamics Flashcards

1
Q

Define System, Model and Simulation

A

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

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2
Q

What constitutes a good model?

A
  • Fast
  • Accurate
  • Time reversible

Since Newton’s eqn of motion is time reversible

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3
Q

Describe the basic algorithm of MD

A
  1. Initialization -Read OFF the pre-set variables such as:
    initial position, velocity (MB distribution).. Temperature etc.
    boundary condition, pair potential…
  2. Calculate Force -Integration of Newton’s equation of motion F=ma
  3. Move particles and update time - Integrators [e. g. varlet or leapfrog] and wait until equilibrium is reached
  4. Output the data: Observables (Temp, Pressure, Energy, )
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4
Q

How is MD initialized?

A
  • 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
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5
Q

Write down and Explain Maxwell-Boltzmann Distribution

A
  • 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
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6
Q

What are boundary conditions?

A

Boundary conditions are parameters or limits that can make calculation of force faster, some examples are;

  • critical radius
  • hard sphere
  • periodic box
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7
Q

What is cut off radius?

A
  • 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
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8
Q

What are dimensionless units?

A

Because computer only know numbers, dimensionless units are derived from basic parameters which prevents large numeric values from different units

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9
Q

How to choose the best time step?

A
  • 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
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10
Q

Briefly define molecular dynamics

A

Molecular Dynamics is a computer simulation method that analyzed the time evolution of atomic interactions by numerical integration of Newton’s equation of motion

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