Journal Article

FZJ-2020-03082

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Biomolecular Simulation: A Perspective from High Performance Computing

Bolnykh, V. (Corresponding author)FZJ* ; Rothlisberger, U. ; Carloni, P.FZJ*

2020
Wiley-VCH Weinheim

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Please use a persistent id in citations: doi:10.1002/ijch.202000022

Abstract: High‐Performance Computing is impacting on all biomedical sciences, including molecular biophysics. Here, we describe general parallel computing strategies (multi‐threading and distributed computing) used in all the natural sciences, including molecular biophysics. Next, we describe how these strategies are applied in molecular dynamics simulations and enhanced sampling methods, either based on force fields, on density functional theory or on QM/MM potentials. As test cases, we focus on the widely used CPMD and GROMACS packages, along with a hybrid QM/MM interface coupling the two recently developed by a European team including the Authors. The review closes with a short perspective on the use of HPC‐based biomolecular simulations.

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Contributing Institute(s):

1. Computational Biomedicine (IAS-5)
2. Computational Biomedicine (INM-9)

Research Program(s):

1. 574 - Theory, modelling and simulation (POF3-574) (POF3-574)
2. DFG project 291198853 - FOR 2518: Funktionale Dynamik von Ionenkanälen und Transportern - DynIon - (291198853)

Appears in the scientific report 2020

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Database coverage:
; Clarivate Analytics Master Journal List ; Current Contents - Physical, Chemical and Earth Sciences ; DEAL Wiley ; Ebsco Academic Search ; Essential Science Indicators ; IF < 5 ; JCR ; NCBI Molecular Biology Database ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Web of Science Core Collection

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