Molecular dynamics is the most popular method used in computational nanotechnology.

Answer the following questions:

a$)$ Describe, Equilibrium Molecular dynamics $($EMD$),$ non$-$equilibrium molecular

dynamics $($NEMD$)$and grand canonical molecular dynamics $($GCMD$).$

b$)$ Draw a simple flowchart that shows the calculations in a typical MD simulation.

c$)$ Name two commonly used schemes for integrating equations of motion. Describe one

of these numerical schemes in detail. What are the advantages and disadvantages of

each scheme?

d$)$ Using a diagram, describe what you know about periodic boundary conditions $($PBC$),$

in the context of molecular simulations. Also, describe the minimum image

convention in keeping track of particle interactions.

e$)$ What is the most computationally intensive part of an MD algorithm? How does the

computation scale up with the number of atoms in a typical simulation?

f$)$ Describe the Verlet list using a diagram and a procedure to decide when to update the

list during a typical MD calculation.