Discuss the basic idea of MD simulation that distinguishes it from quantum mechanics calculation. Using this...

 

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Discuss the basic idea of MD simulation that distinguishes it from quantum mechanics calculation. Using this concept, derive the equation of motion to produce an algorithm integrating a numerical solution in order to predict the trajectory of the atoms or molecules in a system. Explain the advantages of this algorithm. A real system usually contains a massive number of atoms which is impossible to translate into simulation. On the other hand, using a small system creates an interference in the simulation. Discuss these limitations with an example for each, supported with mathematical calculation. Propose and explain a technique to solve this problem. In addition, classical MD technique is time consuming, run at nanoseconds or microseconds requiring millions of energy gradient calculations. Rather than using a high-performance computer to overcome this downside, choose with justification TWO (2) methods that can help to reduce computing time for simulations. Discuss the basic idea of MD simulation that distinguishes it from quantum mechanics calculation. Using this concept, derive the equation of motion to produce an algorithm integrating a numerical solution in order to predict the trajectory of the atoms or molecules in a system. Explain the advantages of this algorithm. A real system usually contains a massive number of atoms which is impossible to translate into simulation. On the other hand, using a small system creates an interference in the simulation. Discuss these limitations with an example for each, supported with mathematical calculation. Propose and explain a technique to solve this problem. In addition, classical MD technique is time consuming, run at nanoseconds or microseconds requiring millions of energy gradient calculations. Rather than using a high-performance computer to overcome this downside, choose with justification TWO (2) methods that can help to reduce computing time for simulations.

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Molecular dynamics MD is a computer simulation method for studying the physical movements of atoms and molecules The atoms and molecules are allowed to interact for a fixed period of time giving rise ... View the full answer