Demonstrating the Transferability and the Descriptive Power of Sketch-Map
Increasingly, it is recognized that new automated forms of analysis are required to understand the high-dimensional output obtained from atomistic simulations. Recently, we introduced a new dimensionality reduction algorithm, sketch-map, that was designed specifically to work with data from molecula...
| Main Authors: | , , |
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| Format: | Journal article |
| Language: | English |
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2013
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| _version_ | 1797069237598027776 |
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| author | Ceriotti, M Tribello, G Parrinello, M |
| author_facet | Ceriotti, M Tribello, G Parrinello, M |
| author_sort | Ceriotti, M |
| collection | OXFORD |
| description | Increasingly, it is recognized that new automated forms of analysis are required to understand the high-dimensional output obtained from atomistic simulations. Recently, we introduced a new dimensionality reduction algorithm, sketch-map, that was designed specifically to work with data from molecular dynamics trajectories. In what follows, we provide more details on how this algorithm works and on how to set its parameters. We also test it on two well-studied Lennard-Jones clusters and show that the coordinates we extract using this algorithm are extremely robust. In particular, we demonstrate that the coordinates constructed for one particular Lennard-Jones cluster can be used to describe the configurations adopted by a second, different cluster and even to tell apart different phases of bulk Lennard-Jonesium. © 2013 American Chemical Society. |
| first_indexed | 2024-03-06T22:21:30Z |
| format | Journal article |
| id | oxford-uuid:5534c685-5f1a-407e-a553-5f428968edd2 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T22:21:30Z |
| publishDate | 2013 |
| record_format | dspace |
| spelling | oxford-uuid:5534c685-5f1a-407e-a553-5f428968edd22022-03-26T16:42:32ZDemonstrating the Transferability and the Descriptive Power of Sketch-MapJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:5534c685-5f1a-407e-a553-5f428968edd2EnglishSymplectic Elements at Oxford2013Ceriotti, MTribello, GParrinello, MIncreasingly, it is recognized that new automated forms of analysis are required to understand the high-dimensional output obtained from atomistic simulations. Recently, we introduced a new dimensionality reduction algorithm, sketch-map, that was designed specifically to work with data from molecular dynamics trajectories. In what follows, we provide more details on how this algorithm works and on how to set its parameters. We also test it on two well-studied Lennard-Jones clusters and show that the coordinates we extract using this algorithm are extremely robust. In particular, we demonstrate that the coordinates constructed for one particular Lennard-Jones cluster can be used to describe the configurations adopted by a second, different cluster and even to tell apart different phases of bulk Lennard-Jonesium. © 2013 American Chemical Society. |
| spellingShingle | Ceriotti, M Tribello, G Parrinello, M Demonstrating the Transferability and the Descriptive Power of Sketch-Map |
| title | Demonstrating the Transferability and the Descriptive Power of Sketch-Map |
| title_full | Demonstrating the Transferability and the Descriptive Power of Sketch-Map |
| title_fullStr | Demonstrating the Transferability and the Descriptive Power of Sketch-Map |
| title_full_unstemmed | Demonstrating the Transferability and the Descriptive Power of Sketch-Map |
| title_short | Demonstrating the Transferability and the Descriptive Power of Sketch-Map |
| title_sort | demonstrating the transferability and the descriptive power of sketch map |
| work_keys_str_mv | AT ceriottim demonstratingthetransferabilityandthedescriptivepowerofsketchmap AT tribellog demonstratingthetransferabilityandthedescriptivepowerofsketchmap AT parrinellom demonstratingthetransferabilityandthedescriptivepowerofsketchmap |