Setting up and Running a Molecular Dynamics Simulation

In this section we will examine some of the steps involved in performing a molecular dynamics simulation in the microcanonical ensemble First, it is necessary to establish an 

One option is to first generate two random numbers and 62 between 0 and 1. The corresponding two numbers from the normal distribution are then calculated using 

An alternative approach is to generate twelve random numbers, . 62 and then calculate  

These two methods generate random numbers in the normal distribution with zero mean and unit variance. A number (x) generated from this distribution can be related to its counterpart (x ) from another Gaussian distribution with mean (x ) and variance a using 

The initial velocities may also be chosen from a uniform distribution or from a simple Gaussian distribution. In either case the Maxwell-Boltzmann distribution of velocities is usually rapidly achieved. 

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Molecular dynamics simulations can overcome energy barriers and provide information about the time-dependent motion of molecular systems. You can use various strategies to set up and run a molecular dynamics simulation, depending on your objective. This section defines many of these strategies and discusses specific considerations in setting up a simulation. 

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