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GPU-Accelerated Computing with Python 3 and CUDA
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Potential energy determines how particles interact in any physical system. Like water that flows downhill, a system tends to evolve to a state of minimal potential. Forces experienced by particles can be derived from the negative gradient of the potential with respect to their positions. Forces give rise to the motion of the particles, and this will be a direction that reduces the potential.
To calculate the potential energy between atoms, we use a set of mathematical functions and parameters. It captures the effects of bonded and non-bonded interactions between atoms as a function of their separation distance. The parameters for potential are obtained from either experimental data or quantum mechanical calculations. In what follows, we will discuss an example of the Lennard-Jones potential, corresponding forces, and how to parallelize the force calculations.
Here, we consider the Lennard-Jones (LJ) potential, which is a simplified model...