A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields
A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields
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DOI：
10.1063/1.479049
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发表时间：
1999-06-01
影响因子：
4.4
通讯作者：
Parrinello, M
中科院分区：
文献类型：
--
作者：
Eichinger, M;Tavan, P;Parrinello, M
我们提出了一种混合方法，用于模拟复杂溶剂中的溶质，例如，通过酶内的底物来表示。该方法结合了溶质的量子力学(QM)描述和溶剂的分子力学(MM)方法。用基于平面波展开式的从头算密度泛函理论(DFT)对模拟系统的QM碎片进行了处理。用计算高效的快速多极方法处理了MM碎片内以及QM和MM碎片之间的长程库仑相互作用。对于两个片段之间的共价键的描述，我们引入了标度位置键原子方法(SPLAM)，它克服了相关方法的缺点。通过对液态水、水二聚体、乙烷和与视网膜席夫碱相关的小分子的测试计算，仔细研究了混合方法的各个方面。特别是，检查了由DFT获得的溶质的振动光谱可能被较低质量的溶剂力场破坏的程度，包括两个碎片共价连接的情况。结果表明，我们的QM/MM混合方法特别适用于凝聚相分子的振动分析。(C)1999年美国物理研究所。[S0021-9606(99)71521-7]。
We present a hybrid method for molecular dynamics simulations of solutes in complex solvents as represented, for example, by substrates within enzymes. The method combines a quantum mechanical (QM) description of the solute with a molecular mechanics (MM) approach for the solvent. The QM fragment of a simulation system is treated by ab initio density functional theory (DFT) based on plane- wave expansions. Long-range Coulomb interactions within the MM fragment and between the QM and the MM fragment are treated by a computationally efficient fast multipole method. For the description of covalent bonds between the two fragments, we introduce the scaled position link atom method (SPLAM), which removes the shortcomings of related procedures. The various aspects of the hybrid method are scrutinized through test calculations on liquid water, the water dimer, ethane and a small molecule related to the retinal Schiff base. In particular, the extent to which vibrational spectra obtained by DFT for the solute can be spoiled by the lower quality force field of the solvent is checked, including cases in which the two fragments are covalently joined. The results demonstrate that our QM/MM hybrid method is especially well suited for the vibrational analysis of molecules in condensed phase. (C) 1999 American Institute of Physics. [S0021-9606(99)71521- 7].