Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature
We apply the non-Markov-type analysis of state-to-state transitions to nearly microsecond molecular dynamics (MD) simulation data at a folding temperature of a small artificial protein, chignolin, and we found that the time scales obtained are consistent with our previous result using the weighted e...
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| Format: | Article |
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MDPI AG
2022-08-01
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| Online Access: | https://www.mdpi.com/2075-1729/12/8/1188 |
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| author | Hiroshi Fujisaki Hiromichi Suetani Luca Maragliano Ayori Mitsutake |
| author_facet | Hiroshi Fujisaki Hiromichi Suetani Luca Maragliano Ayori Mitsutake |
| author_sort | Hiroshi Fujisaki |
| collection | DOAJ |
| description | We apply the non-Markov-type analysis of state-to-state transitions to nearly microsecond molecular dynamics (MD) simulation data at a folding temperature of a small artificial protein, chignolin, and we found that the time scales obtained are consistent with our previous result using the weighted ensemble simulations, which is a general path-sampling method to extract the kinetic properties of molecules. Previously, we also applied diffusion map (DM) analysis, which is one of a manifold of learning techniques, to the same trajectory of chignolin in order to cluster the conformational states and found that DM and relaxation mode analysis give similar results for the eigenvectors. In this paper, we divide the same trajectory into shorter pieces and further apply DM to such short-length trajectories to investigate how the obtained eigenvectors are useful to characterize the conformational change of chignolin. |
| first_indexed | 2024-03-09T13:05:59Z |
| format | Article |
| id | doaj.art-b5bea2f387dc41959cbc545fd8834b6f |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-09T13:05:59Z |
| publishDate | 2022-08-01 |
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| record_format | Article |
| series | Life |
| spelling | doaj.art-b5bea2f387dc41959cbc545fd8834b6f2023-11-30T21:49:17ZengMDPI AGLife2075-17292022-08-01128118810.3390/life12081188Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High TemperatureHiroshi Fujisaki0Hiromichi Suetani1Luca Maragliano2Ayori Mitsutake3Department of Physics, Nippon Medical School, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-0023, JapanDepartment of Integrated Science and Technology, Faculty of Science and Technology, Oita University, 700 Dannoharu, Oita 870-1192, JapanDepartment of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, ItalyDepartment of Physics, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki 214-8571, JapanWe apply the non-Markov-type analysis of state-to-state transitions to nearly microsecond molecular dynamics (MD) simulation data at a folding temperature of a small artificial protein, chignolin, and we found that the time scales obtained are consistent with our previous result using the weighted ensemble simulations, which is a general path-sampling method to extract the kinetic properties of molecules. Previously, we also applied diffusion map (DM) analysis, which is one of a manifold of learning techniques, to the same trajectory of chignolin in order to cluster the conformational states and found that DM and relaxation mode analysis give similar results for the eigenvectors. In this paper, we divide the same trajectory into shorter pieces and further apply DM to such short-length trajectories to investigate how the obtained eigenvectors are useful to characterize the conformational change of chignolin.https://www.mdpi.com/2075-1729/12/8/1188molecular dynamics simulationrare eventMarkov state modelnon-Markov-type analysisdiffusion mapweighted ensemble simulation |
| spellingShingle | Hiroshi Fujisaki Hiromichi Suetani Luca Maragliano Ayori Mitsutake Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature Life molecular dynamics simulation rare event Markov state model non-Markov-type analysis diffusion map weighted ensemble simulation |
| title | Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature |
| title_full | Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature |
| title_fullStr | Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature |
| title_full_unstemmed | Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature |
| title_short | Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature |
| title_sort | non markov type analysis and diffusion map analysis for molecular dynamics trajectory of chignolin at a high temperature |
| topic | molecular dynamics simulation rare event Markov state model non-Markov-type analysis diffusion map weighted ensemble simulation |
| url | https://www.mdpi.com/2075-1729/12/8/1188 |
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