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Copy file name to clipboardExpand all lines: paper/basic_training.tex
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@@ -437,7 +437,7 @@ \subsubsection{Key concepts}
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These interactions are often present but reduced, though the exact amount of reduction differs by the energy function or force field family.
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For example, the AMBER family force fields usually reduce 1-4 electrostatics to $\frac{1}{1.2}$ of their original value, and 1-4 Lennard-Jones interactions to $\frac{1}{2}$ of their original value.
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1-4 interactions are essentially considered the borderline between the bonded and non-bonded regions.
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Because these are short-range interactions, they are potentially quite strong and there is potentially a risk of them overwhelming longer-range interactions, hence their typical reduction.
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These short-range interactions can be quite strong and there is potentially a risk of them overwhelming longer-range interactions, hence their typical reduction.
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%\end{itemize}
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While the number of type of bonded interactions remain unchanged during an MD simulation, the strength and importance of non-bonded interactions varies substantially as a simulation proceeds.
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Additionally, Coulombic interactions fall off only very slowly with distance, as $r^{-1} $, further complicating handling of non-bonded interactions in two different ways.
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First, calculating all Coulomb interactions over a periodic system results in needing to compute a sum which is conditionally convergent --- that is, the value of the sum depends on the order in which it is evaluated~\cite{LeachBook}, meaning we must exercise extreme care or the result will be ambiguous.
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First, calculating all Coulomb interactions over a periodic system results in needing to compute a sum which is conditionally convergent --- that is, the value of the sum depends on the order \emph{in which it is evaluated}~\cite{LeachBook}, meaning we must exercise extreme care or the result will be ambiguous.
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Second, long-range interactions may be relevant, but determining pairwise distances is an expensive computation that grows with the square of the number of atoms involved.
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