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@ARTICLE{Bolnykh:884081,
      author       = {Bolnykh, Viacheslav and Rothlisberger, Ursula and Carloni,
                      Paolo},
      title        = {{B}iomolecular {S}imulation: {A} {P}erspective from {H}igh
                      {P}erformance {C}omputing},
      journal      = {Israel journal of chemistry},
      volume       = {60},
      number       = {7},
      issn         = {1869-5868},
      address      = {Weinheim},
      publisher    = {Wiley-VCH},
      reportid     = {FZJ-2020-03082},
      pages        = {694 - 704},
      year         = {2020},
      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.},
      cin          = {IAS-5 / INM-9},
      ddc          = {540},
      cid          = {I:(DE-Juel1)IAS-5-20120330 / I:(DE-Juel1)INM-9-20140121},
      pnm          = {574 - Theory, modelling and simulation (POF3-574) / DFG
                      project 291198853 - FOR 2518: Funktionale Dynamik von
                      Ionenkanälen und Transportern - DynIon -},
      pid          = {G:(DE-HGF)POF3-574 / G:(GEPRIS)291198853},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000535054900001},
      doi          = {10.1002/ijch.202000022},
      url          = {https://juser.fz-juelich.de/record/884081},
}