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1. Provide a half page summary of this paper?
2. What are the different objectives of molecular dynamics modeling? Clearly explain.
3. Which molecular interaction potentials make up the total potential energy function? Clearly state these.
4. Define and briefly explain the different bonded interactions.
5. Define and briefly explain the different non-bonded interactions.
6. Which algorithm is the most popular to solve the molecular dynamics simulation? What are the key reasons for its usage in the molecular dynamics field?
7. What are periodic boundary conditions and how are they applied in this paper. State briefly.

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1. The “Introduction to Molecular Dynamics Simulation” by Mr. Michael P. Allen gives broad insights of the essential elements needed to perform molecular dynamic simulation, with prominence on macromolecular systems. It is clearly understood that molecular dynamics is used to predict the trajectories of molecules by numerically modeling Newton’s equations of motion for systems of interacting particles, where forces are defined by their interatomic potentials. The forms of intermolecular potential for molecules such as the bonding potential and non-bonding potential were discussed through illustrations and clear derivations of the forces acting on a simple atomic system....
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