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| Main Authors: | , |
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| Format: | Preprint |
| Published: |
2021
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2112.04061 |
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| _version_ | 1866918064519380992 |
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| author | Ortíz, Alberto Pérez de Alba Ensing, Bernd |
| author_facet | Ortíz, Alberto Pérez de Alba Ensing, Bernd |
| contents | We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths and repulsive walkers (multiPMD). We illustrate multiPMD for two C7eq-to-C7ax paths in Ace-Ala-Nme and six PPII-to-PPII paths in Ace-(Pro)4-Nme. We also show a scheme to render an interpretable "PathMap", showing the free energy ridges between paths, as well as the branching and merging of the transition channels. MultiPMD is a flexible and promising method for systems with competing or controversial pathways, which appear in many biomolecular systems, including proteins and nucleic acids. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2112_04061 |
| institution | arXiv |
| publishDate | 2021 |
| record_format | arxiv |
| spellingShingle | Simultaneous sampling of multiple transition channels using adaptive paths of collective variables Ortíz, Alberto Pérez de Alba Ensing, Bernd Statistical Mechanics We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths and repulsive walkers (multiPMD). We illustrate multiPMD for two C7eq-to-C7ax paths in Ace-Ala-Nme and six PPII-to-PPII paths in Ace-(Pro)4-Nme. We also show a scheme to render an interpretable "PathMap", showing the free energy ridges between paths, as well as the branching and merging of the transition channels. MultiPMD is a flexible and promising method for systems with competing or controversial pathways, which appear in many biomolecular systems, including proteins and nucleic acids. |
| title | Simultaneous sampling of multiple transition channels using adaptive paths of collective variables |
| topic | Statistical Mechanics |
| url | https://arxiv.org/abs/2112.04061 |