Essential energy space random walk via energy space metadynamics method to accelerate molecular dynamics simulations

2007 ◽  
Vol 127 (9) ◽  
pp. 094101 ◽  
Author(s):  
Hongzhi Li ◽  
Donghong Min ◽  
Yusong Liu ◽  
Wei Yang
Keyword(s):  
Molecular Dynamics ◽  
Random Walk ◽  
Molecular Dynamics Simulations ◽  
Energy Space ◽  
Dynamics Simulations

scholarly journals Effects of number of parallel runs and frequency of bias-strength replacement in generalized ensemble molecular dynamics simulations

2019 ◽  
Vol 1 ◽  
pp. e4 ◽  
Author(s):  
Takuya Shimato ◽  
Kota Kasahara ◽  
Junichi Higo ◽  
Takuya Takahashi
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
High Frequency ◽  
Md Simulations ◽  
Energy Space ◽  
Bias Potential ◽  
Ensemble Approach ◽  
Dynamics Simulations

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.

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