Hierarchical parallelization of divide-and-conquer density functional tight-binding molecular dynamics and metadynamics simulations

被引:11
|
作者
Nishimura, Yoshifumi [1 ]
Nakai, Hiromi [1 ,2 ,3 ]
机构
[1] Waseda Univ, Waseda Res Inst Sci & Engn, Tokyo, Japan
[2] Waseda Univ, Sch Adv Sci & Engn, Dept Chem & Biochem, Tokyo, Japan
[3] Kyoto Univ, Elements Strategy Initiat Catalysts & Batteries, Kyoto, Japan
关键词
density functional tight-binding method; divide-and-conquer method; metadynamics; molecular dynamics; replica exchange method; C-N BOND; ENHANCED SAMPLING TECHNIQUES; INTERNAL-ROTATION BARRIER; REPLICA-EXCHANGE METHOD; AB-INITIO; GAS-PHASE; THEORETICAL-ANALYSIS; GLOBAL OPTIMIZATION; ION DIFFUSION; FORMAMIDE;
D O I
10.1002/jcc.26217
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Massively parallel divide-and-conquer density functional tight-binding (DC-DFTB) molecular dynamics and metadynamics simulations are efficient approaches for describing various chemical reactions and dynamic processes of large complex systems via quantum mechanics. In this study, DC-DFTB simulations were combined with multi-replica techniques. Specifically, multiple walkers metadynamics, replica exchange molecular dynamics, and parallel tempering metadynamics methods were implemented hierarchically into the in-house Dcdftbmd program. Test simulations in an aqueous phase of the internal rotation of formamide and conformational changes of dialanine showed that the newly developed extensions increase the sampling efficiency and the exploration capabilities in DC-DFTB configuration space.
引用
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页码:1759 / 1772
页数:14
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