Characterization of Rare Events in Molecular Dynamics
A good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2013-12-01
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| Series: | Entropy |
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| Online Access: | http://www.mdpi.com/1099-4300/16/1/350 |
| _version_ | 1798005935504883712 |
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| author | Carsten Hartmann Ralf Banisch Marco Sarich Tomasz Badowski Christof Schütte |
| author_facet | Carsten Hartmann Ralf Banisch Marco Sarich Tomasz Badowski Christof Schütte |
| author_sort | Carsten Hartmann |
| collection | DOAJ |
| description | A good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various algorithms have been proposed for efficiently computing mean first passage times, transition rates or reaction pathways. This article surveys and discusses recent developments in the field of rare event simulation and outlines a new approach that combines ideas from optimal control and statistical mechanics. The optimal control approach described in detail resembles the use of Jarzynski’s equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically) giving variance-free estimators of the rare events statistics. We illustrate the new approach with two numerical examples and discuss its relation to existing methods. |
| first_indexed | 2024-04-11T12:46:59Z |
| format | Article |
| id | doaj.art-faccba55a07247de8fdb4d2a15bf5195 |
| institution | Directory Open Access Journal |
| issn | 1099-4300 |
| language | English |
| last_indexed | 2024-04-11T12:46:59Z |
| publishDate | 2013-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Entropy |
| spelling | doaj.art-faccba55a07247de8fdb4d2a15bf51952022-12-22T04:23:19ZengMDPI AGEntropy1099-43002013-12-0116135037610.3390/e16010350e16010350Characterization of Rare Events in Molecular DynamicsCarsten Hartmann0Ralf Banisch1Marco Sarich2Tomasz Badowski3Christof Schütte4Institut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, GermanyInstitut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, GermanyInstitut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, GermanyInstitut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, GermanyInstitut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, GermanyA good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various algorithms have been proposed for efficiently computing mean first passage times, transition rates or reaction pathways. This article surveys and discusses recent developments in the field of rare event simulation and outlines a new approach that combines ideas from optimal control and statistical mechanics. The optimal control approach described in detail resembles the use of Jarzynski’s equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically) giving variance-free estimators of the rare events statistics. We illustrate the new approach with two numerical examples and discuss its relation to existing methods.http://www.mdpi.com/1099-4300/16/1/350rare eventsmolecular dynamicsoptimal pathwaysstochastic controldynamic programmingchange of measurecumulant generating function |
| spellingShingle | Carsten Hartmann Ralf Banisch Marco Sarich Tomasz Badowski Christof Schütte Characterization of Rare Events in Molecular Dynamics Entropy rare events molecular dynamics optimal pathways stochastic control dynamic programming change of measure cumulant generating function |
| title | Characterization of Rare Events in Molecular Dynamics |
| title_full | Characterization of Rare Events in Molecular Dynamics |
| title_fullStr | Characterization of Rare Events in Molecular Dynamics |
| title_full_unstemmed | Characterization of Rare Events in Molecular Dynamics |
| title_short | Characterization of Rare Events in Molecular Dynamics |
| title_sort | characterization of rare events in molecular dynamics |
| topic | rare events molecular dynamics optimal pathways stochastic control dynamic programming change of measure cumulant generating function |
| url | http://www.mdpi.com/1099-4300/16/1/350 |
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