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Report No.

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, Okumura (2008)) simulation was recently developed as an improved generalized ensemble (GE) methods to focus sampling only on a part of a system (GEPS); he expected that the focused sampling reduced the energy space to be sampled and concomitantly increased the efficiency of the conformational sampling. However, the partial McMD has not been tested well except for an alanine dipeptide system. 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 of the peptide conformation over a conventional GE by scaling of a partial potential energy: electrostatic, van der Waals, and torsion energies relevant to the peptide. We believe that ALSD is an effective method and is applicable to the conformational sampling of larger and more complicated biomolecule systems. Furthermore, ALSD can be available for conformational sampling of biomolecules with intrinsically disordered regions.



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