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Dcdftbmd:用于巨体系量子力学分子动力学模拟的分而治之密度泛函紧束缚程序。

Dcdftbmd: Divide-and-Conquer Density Functional Tight-Binding Program for Huge-System Quantum Mechanical Molecular Dynamics Simulations.

机构信息

Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.

Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.

出版信息

J Comput Chem. 2019 Jun 5;40(15):1538-1549. doi: 10.1002/jcc.25804. Epub 2019 Mar 3.

Abstract

Dcdftbmd is a Fortran 90/95 program that enables efficient quantum mechanical molecular dynamics (MD) simulations using divide-and-conquer density functional tight-binding (DC-DFTB) method. Based on the remarkable performance of previous massively parallel DC-DFTB energy and gradient calculations for huge systems, the code has been specialized to MD simulations. Recent implementations and modifications including DFTB extensions, improved computational speed in the DC-DFTB computational steps, algorithms for efficient initial guess charge prediction, and free energy calculations via metadynamics technique have enhanced the capability to obtain atomistic insights in novel applications to nanomaterials and biomolecules. The energy, structure, and other molecular properties are also accessible through the single-point calculation, geometry optimization, and vibrational frequency analysis. The available functionalities are outlined together with efficiency tests and simulation examples. © 2019 Wiley Periodicals, Inc.

摘要

Dcdftbmd 是一个 Fortran 90/95 程序,它使用分治密度泛函紧束缚(DC-DFTB)方法实现了高效的量子力学分子动力学(MD)模拟。基于先前在大规模并行 DC-DFTB 能量和梯度计算方面对于庞大系统的卓越性能,该代码已专门针对 MD 模拟进行了优化。最近的实现和修改包括 DFTB 扩展、在 DC-DFTB 计算步骤中提高计算速度、用于有效初始猜测电荷预测的算法以及通过元动力学技术进行自由能计算,这些都增强了在纳米材料和生物分子等新应用中获得原子级见解的能力。通过单点计算、几何优化和振动频率分析,也可以获得能量、结构和其他分子性质。本文概述了可用的功能,并进行了效率测试和模拟示例。© 2019 威利父子公司

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