TY - JOUR
T1 - Hierarchical parallelization of divide-and-conquer density functional tight-binding molecular dynamics and metadynamics simulations
AU - Nishimura, Yoshifumi
AU - Nakai, Hiromi
N1 - Funding Information:
This study was supported in part by MEXT as a “Priority Issue on Post-K computer” (Development of new fundamental technologies for high-efficiency energy creation, conversion/storage, and use) and by a Grant-in-Aid for Scientific Research (S) “KAKENHI Grant Number JP18H05264” and a Grant-in-Aid for Specially Promoted Research “KAKENHI Grant Number JP15H05701.” Some computations were performed using the computational resources of the Research Center for Computational Science, Okazaki, Japan.
Funding Information:
This study was supported in part by MEXT as a “Priority Issue on Post‐K computer” (Development of new fundamental technologies for high‐efficiency energy creation, conversion/storage, and use) and by a Grant‐in‐Aid for Scientific Research (S) “KAKENHI Grant Number JP18H05264” and a Grant‐in‐Aid for Specially Promoted Research “KAKENHI Grant Number JP15H05701.” Some computations were performed using the computational resources of the Research Center for Computational Science, Okazaki, Japan.
Publisher Copyright:
© 2020 Wiley Periodicals, Inc.
PY - 2020/7/15
Y1 - 2020/7/15
N2 - 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.
AB - 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.
KW - density functional tight-binding method
KW - divide-and-conquer method
KW - metadynamics
KW - molecular dynamics
KW - replica exchange method
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U2 - 10.1002/jcc.26217
DO - 10.1002/jcc.26217
M3 - Article
C2 - 32358918
AN - SCOPUS:85084212431
SN - 0192-8651
VL - 41
SP - 1759
EP - 1772
JO - Journal of Computational Chemistry
JF - Journal of Computational Chemistry
IS - 19
ER -