Effective data-driven collective variables for free energy calculations from metadynamics of paths
© The Author(s) 2024. Published by Oxford University Press on behalf of National Academy of Sciences..
A variety of enhanced sampling (ES) methods predict multidimensional free energy landscapes associated with biological and other molecular processes as a function of a few selected collective variables (CVs). The accuracy of these methods is crucially dependent on the ability of the chosen CVs to capture the relevant slow degrees of freedom of the system. For complex processes, finding such CVs is the real challenge. Machine learning (ML) CVs offer, in principle, a solution to handle this problem. However, these methods rely on the availability of high-quality datasets-ideally incorporating information about physical pathways and transition states-which are difficult to access, therefore greatly limiting their domain of application. Here, we demonstrate how these datasets can be generated by means of ES simulations in trajectory space via the metadynamics of paths algorithm. The approach is expected to provide a general and efficient way to generate efficient ML-based CVs for the fast prediction of free energy landscapes in ES simulations. We demonstrate our approach with two numerical examples, a 2D model potential and the isomerization of alanine dipeptide, using deep targeted discriminant analysis as our ML-based CV of choice.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2024 |
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| Erschienen: |
2024 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:3 |
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| Enthalten in: |
PNAS nexus - 3(2024), 4 vom: 26. Apr., Seite pgae159 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Müllender, Lukas [VerfasserIn] |
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| Links: |
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| Themen: |
Collective variables |
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| Anmerkungen: |
Date Revised 27.04.2024 published: Electronic-eCollection Citation Status PubMed-not-MEDLINE |
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| doi: |
10.1093/pnasnexus/pgae159 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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NLM371540070 |
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| 520 | |a © The Author(s) 2024. Published by Oxford University Press on behalf of National Academy of Sciences. | ||
| 520 | |a A variety of enhanced sampling (ES) methods predict multidimensional free energy landscapes associated with biological and other molecular processes as a function of a few selected collective variables (CVs). The accuracy of these methods is crucially dependent on the ability of the chosen CVs to capture the relevant slow degrees of freedom of the system. For complex processes, finding such CVs is the real challenge. Machine learning (ML) CVs offer, in principle, a solution to handle this problem. However, these methods rely on the availability of high-quality datasets-ideally incorporating information about physical pathways and transition states-which are difficult to access, therefore greatly limiting their domain of application. Here, we demonstrate how these datasets can be generated by means of ES simulations in trajectory space via the metadynamics of paths algorithm. The approach is expected to provide a general and efficient way to generate efficient ML-based CVs for the fast prediction of free energy landscapes in ES simulations. We demonstrate our approach with two numerical examples, a 2D model potential and the isomerization of alanine dipeptide, using deep targeted discriminant analysis as our ML-based CV of choice | ||
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| 700 | 1 | |a Rizzi, Andrea |e verfasserin |4 aut | |
| 700 | 1 | |a Parrinello, Michele |e verfasserin |4 aut | |
| 700 | 1 | |a Carloni, Paolo |e verfasserin |4 aut | |
| 700 | 1 | |a Mandelli, Davide |e verfasserin |4 aut | |
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