{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T15:34:44Z","timestamp":1772206484555,"version":"3.50.1"},"reference-count":30,"publisher":"SAGE Publications","issue":"6","license":[{"start":{"date-parts":[[2016,7,27]],"date-time":"2016-07-27T00:00:00Z","timestamp":1469577600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["The International Journal of High Performance Computing Applications"],"published-print":{"date-parts":[[2017,11]]},"abstract":"<jats:p> A novel perturbative Monte Carlo mixed quantum mechanics (QM)\/molecular mechanics (MM) approach has been recently developed to simulate molecular systems in complex environments. However, the required accuracy to efficiently simulate such complex molecular systems is usually granted at the cost of long executing times. To alleviate this problem, a new parallelization strategy of multi-level Monte Carlo molecular simulations is herein proposed for heterogeneous systems. It simultaneously exploits fine-grained (at the data level), coarse-grained (at the Markov chain level) and task-grained (pure QM, pure MM and QM\/MM procedures) parallelism to ensure an efficient execution in heterogeneous systems composed of central processing units and multiple and possibly different graphical processing units. This is achieved by making use of the OpenCL library, together with appropriate dynamic load balancing schemes. From the conducted evaluation with real benchmarking data, a speed-up of 56x in the computational bottleneck part was observed, which results in a global speed-up of 38x for the whole simulation, reducing the time of a typical simulation from 80 hours to only 2 hours. <\/jats:p>","DOI":"10.1177\/1094342016649420","type":"journal-article","created":{"date-parts":[[2016,5,31]],"date-time":"2016-05-31T00:08:23Z","timestamp":1464653303000},"page":"499-516","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":2,"title":["Efficient parallelization of perturbative Monte Carlo QM\/MM simulations in heterogeneous platforms"],"prefix":"10.1177","volume":"31","author":[{"given":"Sebasti\u00e3o","family":"Miranda","sequence":"first","affiliation":[{"name":"INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal"}]},{"given":"Jonas","family":"Feldt","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Physikalische Chemie, Universit\u00e4t G\u00f6ttingen, G\u00f6ttingen, Germany"}]},{"given":"Frederico","family":"Pratas","sequence":"additional","affiliation":[{"name":"INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal"}]},{"given":"Ricardo A","family":"Mata","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Physikalische Chemie, Universit\u00e4t G\u00f6ttingen, G\u00f6ttingen, Germany"}]},{"given":"Nuno","family":"Roma","sequence":"additional","affiliation":[{"name":"INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal"}]},{"given":"Pedro","family":"Tom\u00e1s","sequence":"additional","affiliation":[{"name":"INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal"}]}],"member":"179","published-online":{"date-parts":[[2016,7,27]]},"reference":[{"key":"bibr1-1094342016649420","doi-asserted-by":"publisher","DOI":"10.1016\/j.cpc.2007.03.004"},{"key":"bibr2-1094342016649420","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcp.2013.07.023"},{"key":"bibr3-1094342016649420","doi-asserted-by":"publisher","DOI":"10.1002\/cpe.1631"},{"key":"bibr4-1094342016649420","doi-asserted-by":"publisher","DOI":"10.1039\/c0ob00691b"},{"key":"bibr5-1094342016649420","doi-asserted-by":"publisher","DOI":"10.1142\/S0129626411000163"},{"key":"bibr6-1094342016649420","doi-asserted-by":"publisher","DOI":"10.1063\/1.2206581"},{"key":"bibr7-1094342016649420","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21209"},{"key":"bibr8-1094342016649420","unstructured":"Geromichalos GD (2007) Importance of molecular computer modeling in anticancer drug development. 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