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UID:submissions.pasc-conference.org_PASC23_sess178_pap138@linklings.com
SUMMARY:Runtime Steering of Molecular Dynamics Simulations Through In Situ
  Analysis and Annotation of Collective Variables
DESCRIPTION:Paper\n\nSilvina Caino-Lores (University of Tennessee); Michel
  Cuendet (Swiss Institute of Bioinformatics, Cornell University); Jack Mar
 quez (University of Tennessee); Ekaterina Kots (Cornell University); Trilc
 e Estrada (University of New Mexico); Ewa Deelman (University of Southern 
 California); Harel Weinstein (Cornell University); and Michela Taufer (Uni
 versity of Tennessee)\n\nThis paper targets one of the most common simulat
 ions on petascale and, very likely, on exascale machines: molecular dynami
 cs (MD) simulations studying the (classical) time evolution of a molecular
  system at atomic resolution. Specifically, this work addresses the data c
 hallenges of MD simulations at exascale through (1) the creation of a data
  analysis method based on a suite of advanced collective variables (CVs) s
 elected for annotation of structural molecular properties and capturing ra
 re conformational events at runtime, (2) the definition of an in situ fram
 ework to automatically identify the frames where the rare events occur dur
 ing an MD simulation and (3) the integration of both method and framework 
 into two MD workflows for the study of early termination or termination an
 d restart of a benchmark molecular system for protein folding -the Fs pept
 ide system (Ace-A_5(AAARA)_3A-NME)- using Summit. The approach achieves fa
 ster exploration of the conformational space compared to extensive ensembl
 e simulations. Specifically, our in situ framework with early termination 
 alone achieves 99.6% coverage of the reference conformational space for th
 e Fs peptide with just ~60% of the MD steps otherwise used for a tradition
 al execution of the MD simulation. Annotation-based restart allows us to c
 over 94.6% of the conformational space, just running 50% of the overall MD
  steps.\n\nDomain: Life Sciences\n\nSession Chair: John Biddiscombe (ETH Z
 urich / CSCS)
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