Hodak Miroslav, Lu Wenchang, Bernholc J
Center for High Performance Simulation and Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-7518, USA.
J Chem Phys. 2008 Jan 7;128(1):014101. doi: 10.1063/1.2814165.
A hybrid computational method intended for simulations of biomolecules in solution is described. The ab initio Kohn-Sham (KS) density functional theory (DFT) method is used to describe the chemically active part of the system and its first solvation shells, while a frozen-density orbital-free (FDOF) DFT method is used to treat the rest of the solvent. The molecules in the FDOF method have fixed internal structures and frozen electron densities. The hybrid method provides a seamless description of the boundary between the subsystems and allows for the flow of molecules across the boundary. Tests on a liquid water system show that the total energy is conserved well during molecular dynamics and that the effect of the solvent environment on the KS subsystem is well described. An initial application to copper ion binding to the prion protein is also presented.
描述了一种用于模拟溶液中生物分子的混合计算方法。从头算的Kohn-Sham（KS）密度泛函理论（DFT）方法用于描述系统的化学活性部分及其第一溶剂化层，而冻结密度无轨道（FDOF）DFT方法用于处理其余的溶剂。FDOF方法中的分子具有固定的内部结构和冻结的电子密度。该混合方法提供了子系统之间边界的无缝描述，并允许分子跨边界流动。对液态水系统的测试表明，在分子动力学过程中总能量守恒良好，并且溶剂环境对KS子系统的影响得到了很好的描述。还展示了该方法在铜离子与朊病毒蛋白结合方面的初步应用。
