How to determine accurate conformational ensembles by metadynamics metainference : A chignolin study case
Articolo
Data di Pubblicazione:
2021
Citazione:
How to determine accurate conformational ensembles by metadynamics metainference : A chignolin study case / C. Paissoni, C. Camilloni. - In: FRONTIERS IN MOLECULAR BIOSCIENCES. - ISSN 2296-889X. - 8(2021 May 26), pp. 694130.1-694130.10.
Abstract:
The reliability and usefulness of molecular dynamics simulations of equilibrium processes rests on their statistical precision and their capability to generate conformational ensembles in agreement with available experimental knowledge. Metadynamics Metainference (M&M), coupling molecular dynamics with the enhanced sampling ability of Metadynamics and with the ability to integrate experimental information of Metainference, can in principle achieve both goals. Here we show that three different Metadynamics setups provide converged estimate of the populations of the three-states
populated by a model peptide. Errors are estimated correctly by block averaging, but higher precision is obtained by performing independent replicates. One effect of Metadynamics is that of dramatically decreasing the number of effective frames resulting from the simulations and this is relevant for M&M where the number of replicas should be large enough to capture the conformational heterogeneity behind the experimental data. Our simulations allow also us to propose that monitoring the relative error associated with conformational averaging can help to determine the minimum number of replicas to be simulated in the context of M&M simulations. Altogether our data provides useful indication on how to generate sound conformational ensemble in
agreement with experimental data.
Tipologia IRIS:
01 - Articolo su periodico
Keywords:
molecular dynamics; metadynamics; metainference; statistical error; conformational ensembles
Elenco autori:
C. Paissoni, C. Camilloni
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