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Computation 2018, 6(1), 15; https://doi.org/10.3390/computation6010015

Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments

Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy
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Received: 15 January 2018 / Revised: 31 January 2018 / Accepted: 1 February 2018 / Published: 6 February 2018
(This article belongs to the Special Issue Computation in Molecular Modeling)
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Abstract

Molecular dynamics (MD) simulations allow the investigation of the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields, it is becoming common to integrate MD simulations with experimental data obtained from ensemble measurements. We review here the approaches that can be used to combine MD and experiment under the guidance of the maximum entropy principle. We mostly focus on methods based on Lagrangian multipliers, either implemented as reweighting of existing simulations or through an on-the-fly optimization. We discuss how errors in the experimental data can be modeled and accounted for. Finally, we use simple model systems to illustrate the typical difficulties arising when applying these methods. View Full-Text
Keywords: molecular dynamics; maximum entropy principle; ensemble averages; experimental constraints molecular dynamics; maximum entropy principle; ensemble averages; experimental constraints
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Cesari, A.; Reißer, S.; Bussi, G. Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments. Computation 2018, 6, 15.

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