Adaptive lambda square dynamics simulation: An efficient conformational sampling method for biomolecules |
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Authors: | Jinzen Ikebe Shun Sakuraba Hidetoshi Kono |
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Affiliation: | Molecular Modeling and Simulation Group, Japan Atomic Energy Agency, 8‐1‐7 Umemidai, Kizugawa, Kyoto, Japan |
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Abstract: | A novel, efficient sampling method for biomolecules is proposed. The partial multicanonical molecular dynamics (McMD) was recently developed as a method that improved generalized ensemble (GE) methods 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 polylysine 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. We believe that ALSD is an effective method and is applicable to the conformational sampling of larger and more complicated biomolecule systems. © 2013 Wiley Periodicals, Inc. |
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Keywords: | generalized ensemble method partial system free energy landscape explicit water all‐atom model |
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