Computation-Based Science and Technology Research Center CaSToRC, The Cyprus Institute , 20 Konstantinou Kavafi Street, 2121, Aglantzia, Nicosia, Cyprus.
Department of Physics, Faculty of Mathematics, Computer Science and Natural Sciences, Aachen University , Otto-Blumenthal-Straße, 52074 Aachen, Germany.
J Chem Theory Comput. 2017 Nov 14;13(11):5647-5657. doi: 10.1021/acs.jctc.7b00508. Epub 2017 Oct 27.
The recently proposed Hamiltonian adaptive resolution scheme (H-AdResS) allows the performance of molecular simulations in an open boundary framework. It allows changing, on the fly, the resolution of specific subsets of molecules (usually the solvent), which are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the molecular mechanics/coarse-grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models. Toward this goal, here we apply for the first time H-AdResS to two atomistic proteins in dual-resolution solvent, proving its ability to reproduce structural and dynamic properties of both the proteins and the solvent, as obtained from atomistic simulations.
最近提出的哈密顿自适应分辨率方案（H-AdResS）允许在开放边界框架中进行分子模拟。它可以在特定分子子集（通常是溶剂）的分辨率上进行实时更改，这些子集可以在原子区域和粗粒储层之间自由扩散。到目前为止，该方法已成功应用于纯液体。将 H-AdResS 方法与蛋白质的混合模型（如分子力学/粗粒化（MM/CG）方案）耦合是一种在低分辨率蛋白质模型中严格计算配体结合自由能的有前途的方法。为此，我们首次将 H-AdResS 应用于双分辨率溶剂中的两个原子蛋白质，证明了它能够重现原子模拟中获得的蛋白质和溶剂的结构和动态特性。
