Fastpka

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fastpka is a pka->clust (ICDA) parameter.

It causes the computes the internal energies for the different cluster states by dividing the protein into "fixed" and "optimized" atoms. Many of the energy terms (all fixed-fixed) interactions can be computed once in advance and stored as they do not change as protonation states change. So what is left to compute are the optimized-optimized terms and the optimized-fixed terms for each state.

There are notes in the source indicating that this code was never finished and does not handle crystal symmetry correctly.

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