3 years ago

An assessment of optimal time scale of conformational resampling for parallel cascade selection molecular dynamics

Ryuhei Harada, Yasuteru Shigeta

Parallel cascade selection molecular dynamics (PaCS-MD) has been proposed as a conformational sampling method for enhancing structural transitions from a given reactant to a product by repeating cycles of short-time MD simulations. In the present paper, we assessed how the time scale of a short-time MD simulation affected the computational efficiency by changing the simulation length. In conclusion, ps-order (tps) PaCS-MD simulations showed a higher computational efficiency as a total simulation time over the cycles than ns-order (tns) PaCS-MD simulations, indicating that tps might be suitable for generating structural transitions efficiently.

Publisher URL: http://www.tandfonline.com/doi/full/10.1080/08927022.2017.1362696

DOI: 10.1080/08927022.2017.1362696

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