Adaptive Resolution Simulations with Self-Adjusting High-Resolution Regions

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• 作者：Karsten Kreis ; Raffaello Potestio ; Kurt Kremer ; Aoife C. Fogarty
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2016
• 出版时间：August 9, 2016
• 年：2016
• 卷：12
• 期：8
• 页码：4067-4081
• 全文大小：1289K
• 年卷期：0
• ISSN：1549-9626

文摘

In adaptive resolution simulations, different regions of a simulation box are modeled with different levels of detail. Particles change their resolution on-the-fly when traveling from one subregion to the other. This method is particularly useful for studying multiscale systems in which effects on a broad range of length and time scales play a role. Until now, the geometry of the high-resolution region has been limited to simple geometries of spherical, cuboid, or cylindrical form, whose shape does not change during the simulation. However, many phenomena involve changes in size and shape of system components, for example, protein folding, polymer collapse, nucleation, and crystallization. In this work, we develop a scheme that uses a series of overlapping spheres to allow for an arbitrary division of space into domains of different levels of resolution. Furthermore, the geometry is automatically adjusted on-the-fly during the simulation according to changes in size and shape of, for example, a solvated macromolecule within the high-resolution region. The proposed approach is validated on liquid water. We then simulate the folding of an atomistically detailed polypeptide solvated in a shell of atomistic water that changes shape as the peptide conformation changes. We demonstrate that the peptide folding process is unperturbed by the use of our methodology.