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CSJ Journals

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2020, Vol.49, No.7

798-801

Regenerations of Initial Velocities in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Enhance the Conformational Transitions of Proteins

Hayato Aida ,1Yasuteru Shigeta ,2 and Ryuhei Harada *2
1Master's Program in Biology , University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-0821, Japan
2Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-0821, Japan
https://doi.org/10.1246/cl.200196

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Abstract

Parallel cascade selection molecular dynamics (PaCS-MD) is a rare event sampling method. PaCS-MD repeats cycles of resampling from important initial structures based on short-time MD simulations. When restarting the short-time MD simulations, regenerations of the initial velocities play an essential role in creating perturbations to promote conformational transitions. Therefore, we addressed the conformational sampling efficiencies of PaCS-MDs with and without the regenerations of initial velocities by modeling the folding of a mini-protein (Chignolin) in explicit water. In the present letter, we confirmed that the regenerations of initial velocities increased the conformational sampling efficiency of PaCS-MD.

figure

PaCS-MD is a rare-event sampling method. PaCS-MD repeats a set of resampling from important initial structures based on short-time MD. In restarting the short-time MD, regenerations of initial velocities are essential because they play a role of perturbations in promoting transitions. In this study, we confirmed that the regenerations of the initial velocities increased the sampling efficiency of PaCS-MD.

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