Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics
Many interesting rare events in molecular systems, like ligand association, protein folding or conformational changes, occur on timescales that often are not accessible by direct numerical simulation. Therefore, rare event approximation approaches like interface sampling, Markov state model building...
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| Format: | Article |
| Language: | English |
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MDPI AG
2017-07-01
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| Series: | Entropy |
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| Online Access: | https://www.mdpi.com/1099-4300/19/7/367 |
| _version_ | 1811307480793219072 |
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| author | Wei Zhang Christof Schütte |
| author_facet | Wei Zhang Christof Schütte |
| author_sort | Wei Zhang |
| collection | DOAJ |
| description | Many interesting rare events in molecular systems, like ligand association, protein folding or conformational changes, occur on timescales that often are not accessible by direct numerical simulation. Therefore, rare event approximation approaches like interface sampling, Markov state model building, or advanced reaction coordinate-based free energy estimation have attracted huge attention recently. In this article we analyze the reliability of such approaches. How precise is an estimate of long relaxation timescales of molecular systems resulting from various forms of rare event approximation methods? Our results give a theoretical answer to this question by relating it with the transfer operator approach to molecular dynamics. By doing so we also allow for understanding deep connections between the different approaches. |
| first_indexed | 2024-04-13T09:05:05Z |
| format | Article |
| id | doaj.art-008ceeb40967472cb9b53421f14419f3 |
| institution | Directory Open Access Journal |
| issn | 1099-4300 |
| language | English |
| last_indexed | 2024-04-13T09:05:05Z |
| publishDate | 2017-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Entropy |
| spelling | doaj.art-008ceeb40967472cb9b53421f14419f32022-12-22T02:53:01ZengMDPI AGEntropy1099-43002017-07-0119736710.3390/e19070367e19070367Reliable Approximation of Long Relaxation Timescales in Molecular DynamicsWei Zhang0Christof Schütte1Institute of Mathematics, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, GermanyInstitute of Mathematics, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, GermanyMany interesting rare events in molecular systems, like ligand association, protein folding or conformational changes, occur on timescales that often are not accessible by direct numerical simulation. Therefore, rare event approximation approaches like interface sampling, Markov state model building, or advanced reaction coordinate-based free energy estimation have attracted huge attention recently. In this article we analyze the reliability of such approaches. How precise is an estimate of long relaxation timescales of molecular systems resulting from various forms of rare event approximation methods? Our results give a theoretical answer to this question by relating it with the transfer operator approach to molecular dynamics. By doing so we also allow for understanding deep connections between the different approaches.https://www.mdpi.com/1099-4300/19/7/367molecular dynamicseigenproblemeffective dynamicsGalerkin methodvariational approachMarkov state modelreaction coordinate |
| spellingShingle | Wei Zhang Christof Schütte Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics Entropy molecular dynamics eigenproblem effective dynamics Galerkin method variational approach Markov state model reaction coordinate |
| title | Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics |
| title_full | Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics |
| title_fullStr | Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics |
| title_full_unstemmed | Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics |
| title_short | Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics |
| title_sort | reliable approximation of long relaxation timescales in molecular dynamics |
| topic | molecular dynamics eigenproblem effective dynamics Galerkin method variational approach Markov state model reaction coordinate |
| url | https://www.mdpi.com/1099-4300/19/7/367 |
| work_keys_str_mv | AT weizhang reliableapproximationoflongrelaxationtimescalesinmoleculardynamics AT christofschutte reliableapproximationoflongrelaxationtimescalesinmoleculardynamics |