... changes¹

Changes in the shape of a protein, i.e. motion

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... molecules²

Molecules used by living organisms; generally containing carbon

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... law³

Coulomb's law:

$$F = \frac{q_{0}q_{1}}{4 \pi \epsilon_0 r^{2}}$$ (1)

relates the distance and charge of particles to the force they produce

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... artifacts⁴

Behaviors introduced by simulation techniques that do not represent actual behavior

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... space⁵

A domain in which it is easier to process periodic functions, for more discussion see [16]

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... question.⁶

A Gaussian is a function similar to a bell curve, concentrated in the middle and falling off towards both extremes.

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... polynomials⁷

The technique used for interpolation in the original PME method put forth in [7], they are only defined at certain points and thus are not differentiable

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... particles⁸

It also has direction; it is a vector

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... vectors⁹

a vector whose magnitude is one

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...¹⁰

Ewald equations adapted from [10]

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...¹¹

PME equation adapted from [7]

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...$u>2$¹²

Cardinal B-Spline equations adapted from [9].

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... expansion¹³

A series of pre-calculated terms that can be used to approximate a function

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