Adaptive lambda square dynamics simulation; An Efficient conformational sampling method for biomolecules

Ikebe, Kimiyoshi; Sakuraba, Shun; Kono, Hidetoshi

A novel, efficient sampling method for biomolecules is proposed. The partial multicanonical molecular dynamics (partial McMD) was recently developed as a generalized ensemble (GE) method to focus sampling only on a part of a system (GEPS); however, it was not tested well. We found that partial McMD did not work well for poly-lysine decapeptide and gave significantly worse sampling efficiency than a conventional GE. Herein, we elucidate the fundamental reason for this and propose a novel GEPS, adaptive lambda square dynamics (ALSD), which can resolve the problem faced when using partial McMD. We demonstrate that ALSD greatly increases the sampling efficiency over a conventional GE.