Write down the formula of the hamiltonian

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1. Describe using no more than 200 words what is a protein and how could we model and simulate it using classical mechanics and computer programs.

2. Write down the formula of the Hamiltonian used in a typical classical atomistic molecular dynamics simulation. Describe the potential energy terms using only one simple sentence for each term.

3. Plot on a single graph the Lennard-Jones potential using the parameters σ=3, and ε1=2, ε2=3 and ε3=4. State in one short sentence what is the interpretation of the parameter ε. Please remember to label your axes properly.

4. Plot on a single graph the Lennard-Jones potential using the parameters ε=3, σ1=2, σ2=3 and σ3=4. State in one short sentence what is the interpretation of the parameter σ. Please remember to label your axes properly.

Reference no: EM13541545

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