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EnglishThe computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strength of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide.
Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering / Gil Ley, Alejandro; Bussi, Giovanni. - In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION. - ISSN 1549-9618. - 11:3(2015), pp. 1077-1085.
| Titolo: | Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering |
| Autori: | Gil Ley, Alejandro; Bussi, Giovanni |
| Rivista: | |
| Data di pubblicazione: | 2015 |
| Volume: | 11 |
| Fascicolo: | 3 |
| Pagina iniziale: | 1077 |
| Pagina finale: | 1085 |
| Digital Object Identifier (DOI): | http://dx.doi.org/10.1021/ct5009087 |
| Fulltext via DOI: | http://dx.doi.org/10.1021/ct5009087 |
| URL: | https://arxiv.org/abs/1502.02115 |
| Appare nelle tipologie: | 1.1 Journal article |
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| File | Descrizione | Tipologia | Licenza | |
|---|---|---|---|---|
| ct5009087.pdf | Versione Editoriale (PDF) | Non specificato | Open Access Visualizza/Apri |
