Abstract
Background The generalized ensemble approach with the molecular dynamics (MD) method has been widely utilized. This approach usually has two features. (i) A bias potential, whose strength is replaced during a simulation, is applied. (ii) Sampling can be performed by many parallel runs of simulations. Although the frequency of the bias-strength replacement and the number of parallel runs can be adjusted, the effects of these settings on the resultant ensemble remain unclear. Method In this study, we performed multicanonical MD simulations for a foldable mini-protein (Trp-cage) and two unstructured peptides (8- and 20-residue poly-glutamic acids) with various settings. Results As a result, running many short simulations yielded robust results for the Trp-cage model. Regarding the frequency of the bias-potential replacement, although using a high frequency enhanced the traversals in the potential energy space, it did not promote conformational changes in all the systems.
Highlights
In the past several decades, the molecular dynamics (MD) method has been widely applied to investigate the microscopic behavior of molecular systems
It is not straightforward to characterize the free-energy landscape (FEL) of a complex molecular system, because the characteristics of conformational ensembles obtained via canonical MD simulations largely depend on the initial conditions
The reference ensemble is characterized in the subsection, “FEL of folding–unfolding equilibrium of Trp-cage.”
Summary
In the past several decades, the molecular dynamics (MD) method has been widely applied to investigate the microscopic behavior of molecular systems. It is not straightforward to characterize the free-energy landscape (FEL) of a complex molecular system, because the characteristics of conformational ensembles obtained via canonical MD simulations largely depend on the initial conditions. To solve this problem, the generalized ensemble (GE) approach has been extensively developed and applied to the MD method. The generalized ensemble approach with the molecular dynamics (MD) method has been widely utilized. The frequency of the bias-strength replacement and the number of parallel runs can be adjusted, the effects of these settings on the resultant ensemble remain unclear. Regarding the frequency of the bias-potential replacement, using a high frequency enhanced the traversals in the potential energy space, it did not promote conformational changes in all the systems
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