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

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.

Keywords:

• Conformational sampling
• molecular dynamics simulation
• parallel cascade
• selection molecular dynamics

Acknowledgements

The computations were partially performed with COMA/HA-PACS at the Center for Computational Sciences (CCS), University of Tsukuba.