Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments
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...
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doaj-ba7a7ad761d04f2195c6abaa2cbeeea02020-11-24T23:44:20ZengMDPI AGComputation2079-31972018-02-01611510.3390/computation6010015computation6010015Using the Maximum Entropy Principle to Combine Simulations and Solution ExperimentsAndrea Cesari0Sabine Reißer1Giovanni Bussi2Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, ItalyScuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, ItalyScuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, ItalyMolecular 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.http://www.mdpi.com/2079-3197/6/1/15molecular dynamicsmaximum entropy principleensemble averagesexperimental constraints |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Andrea Cesari Sabine Reißer Giovanni Bussi |
spellingShingle |
Andrea Cesari Sabine Reißer Giovanni Bussi Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments Computation molecular dynamics maximum entropy principle ensemble averages experimental constraints |
author_facet |
Andrea Cesari Sabine Reißer Giovanni Bussi |
author_sort |
Andrea Cesari |
title |
Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments |
title_short |
Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments |
title_full |
Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments |
title_fullStr |
Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments |
title_full_unstemmed |
Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments |
title_sort |
using the maximum entropy principle to combine simulations and solution experiments |
publisher |
MDPI AG |
series |
Computation |
issn |
2079-3197 |
publishDate |
2018-02-01 |
description |
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. |
topic |
molecular dynamics maximum entropy principle ensemble averages experimental constraints |
url |
http://www.mdpi.com/2079-3197/6/1/15 |
work_keys_str_mv |
AT andreacesari usingthemaximumentropyprincipletocombinesimulationsandsolutionexperiments AT sabinereißer usingthemaximumentropyprincipletocombinesimulationsandsolutionexperiments AT giovannibussi usingthemaximumentropyprincipletocombinesimulationsandsolutionexperiments |
_version_ |
1725499114864508928 |