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research article

Biomolecular Simulation: a Perspective from High Performance Computing

Bolnykh, Viacheslav  
•
Rothlisberger, Ursula  
•
Carloni, Paolo
May 25, 2020
Israel Journal Of Chemistry

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.

Additional information on optimizations and software adjustments to maximize code performance are provided in the Supporting Information.

  • Details
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Type
research article
DOI
10.1002/ijch.202000022
Web of Science ID

WOS:000535054900001

Author(s)
Bolnykh, Viacheslav  
•
Rothlisberger, Ursula  
•
Carloni, Paolo
Date Issued

2020-05-25

Publisher

WILEY-V C H VERLAG GMBH

Published in
Israel Journal Of Chemistry
Volume

60

Issue

7

Start page

694

End page

704

Subjects

Chemistry, Multidisciplinary

•

Chemistry

•

density functional theory

•

molecular mechanics

•

qm

•

mm

•

molecular dynamics

•

massively parallel biomolecular simulations

•

molecular-dynamics simulations

•

replicated data

•

algorithm

•

accuracy

•

forces

Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LCBC  
Available on Infoscience
June 10, 2020
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/169188
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