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arxiv: 1802.06560 · v3 · pith:5S6AI22Rnew · submitted 2018-02-19 · 🧬 q-bio.BM · cond-mat.stat-mech

An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations

classification 🧬 q-bio.BM cond-mat.stat-mech
keywords principlesimulationsdatamaximumreplica-averagedrestrainedentropyexperimental
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Inferential methods can be used to integrate experimental informations and molecular simulations. The maximum entropy principle provides a framework for using equilibrium experimental data and it has been shown that replica-averaged simulations, restrained using a static potential, are a practical and powerful implementation of such principle. Here we show that replica-averaged simulations restrained using a time-dependent potential are equivalent to the principle of maximum caliber, the dynamic version of the principle of maximum entropy, and thus may allow to integrate time-resolved data in molecular dynamics simulations. We provide an analytical proof of the equivalence as well as a computational validation making use of simple models and synthetic data. Some limitations and possible solutions are also discussed.

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