An assessment of optimal time scale of conformational resampling for parallel cascade selection molecular dynamics. Issue 3 (11th February 2018)

• Record Type: Journal Article
• Authors: Harada, Ryuhei; Shigeta, Yasuteru
• Is Part Of: Molecular simulation. Volume 44:Issue 3(2018)
• Page Start: 206
• Page End: 212
• Publication Date: 2018-02-11
• Subjects: Conformational sampling -- molecular dynamics simulation -- parallel cascade -- selection molecular dynamics; Molecular dynamics -- Computer simulation -- Periodicals; Statistical mechanics -- Computer simulation -- Periodicals; 539.6
• DOI: 10.1080/08927022.2017.1362696
• Languages: English
• ISSNs: 0892-7022

Abstract

Abstract: 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 ( t ps ) PaCS-MD simulations showed a higher computational efficiency as a total simulation time over the cycles than ns-order ( t ns ) PaCS-MD simulations, indicating that t ps might be suitable for generating structural transitions efficiently.