This title appears in the Scientific Report :
2020
Please use the identifier:
http://dx.doi.org/10.1002/ijch.202000022 in citations.
Biomolecular Simulation: A Perspective from High Performance Computing
Biomolecular Simulation: A Perspective from High Performance Computing
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 strate...
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Personal Name(s): | Bolnykh, Viacheslav (Corresponding author) |
---|---|
Rothlisberger, Ursula / Carloni, Paolo | |
Contributing Institute: |
Computational Biomedicine; INM-9 Computational Biomedicine; IAS-5 |
Published in: | Israel journal of chemistry, 60 (2020) 7, S. 694 - 704 |
Imprint: |
Weinheim
Wiley-VCH
2020
|
DOI: |
10.1002/ijch.202000022 |
Document Type: |
Journal Article |
Research Program: |
FOR 2518: Funktionale Dynamik von Ionenkanälen und Transportern - DynIon - Theory, modelling and simulation |
Publikationsportal JuSER |
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. |