Literature DB >> 31498615

Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC.

Viacheslav Bolnykh1,2,3, Jógvan Magnus Haugaard Olsen4, Simone Meloni5, Martin P Bircher6, Emiliano Ippoliti3, Paolo Carloni1,3,7, Ursula Rothlisberger6.   

Abstract

We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computation of electrostatic QM/MM interactions is parallelized exploiting both distributed- and shared-memory strategies. Here, we use the efficient CPMD and GROMACS programs as QM and MM engines, respectively. The scalability is demonstrated through large-scale benchmark simulations of realistic biomolecular systems employing non-hybrid and hybrid GGA exchange-correlation functionals. We show that the loose-coupling strategy adopted in MiMiC, with its inherent high flexibility, does not carry any significant computational overhead compared to a tight-coupling scheme. Furthermore, we demonstrate that the adopted parallelization strategy enables scaling up to 13,000 CPU cores with efficiency above 70%, thus making DFT-based QM/MM MD simulations using hybrid functionals at the nanosecond scale accessible.

Year:  2019        PMID: 31498615     DOI: 10.1021/acs.jctc.9b00424

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  2 in total

1.  Dopamine-Decorated TiO2 Nanoparticles in Water: A QM/MM vs an MM Description.

Authors:  Paulo Siani; Stefano Motta; Lorenzo Ferraro; Asmus O Dohn; Cristiana Di Valentin
Journal:  J Chem Theory Comput       Date:  2020-09-17       Impact factor: 6.006

2.  MiMiC: Multiscale Modeling in Computational Chemistry.

Authors:  Viacheslav Bolnykh; Jógvan Magnus Haugaard Olsen; Simone Meloni; Martin P Bircher; Emiliano Ippoliti; Paolo Carloni; Ursula Rothlisberger
Journal:  Front Mol Biosci       Date:  2020-03-20
  2 in total

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