Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk

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• 作者：Leonardo Darr茅 ; Alex Tek ; Marc Baaden ; Sergio Pantano
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2012
• 出版时间：October 9, 2012
• 年：2012
• 卷：8
• 期：10
• 页码：3880-3894
• 全文大小：794K
• 年卷期：v.8,no.10(October 9, 2012)
• ISSN：1549-9626

文摘

Accurate simulation of biomolecular systems requires the consideration of solvation effects. The arrangement and dynamics of water close to a solute are strongly influenced by the solute itself. However, as the solute鈥搒olvent distance increases, the water properties tend to those of the bulk liquid. This suggests that bulk regions can be treated at a coarse grained (CG) level, while keeping the atomistic details around the solute. Since water represents about 80% of any biological system, this approach may offer a significant reduction in the computational cost of simulations without compromising atomistic details. We show here that mixing the popular SPC water model with a CG model for solvation (called WatFour) can effectively mimic the hydration, structure, and dynamics of molecular systems composed of pure water, simple electrolyte solutions, and solvated macromolecules. As a nontrivial example, we present simulations of the SNARE membrane fusion complex, a trimeric protein鈥損rotein complex embedded in a double phospholipid bilayer. Comparison with a fully atomistic reference simulation illustrates the equivalence between both approaches.