{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T13:19:22Z","timestamp":1762867162321,"version":"3.37.3"},"reference-count":33,"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","issue":"2","license":[{"start":{"date-parts":[[2019,3,1]],"date-time":"2019-03-01T00:00:00Z","timestamp":1551398400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/ieeexplore.ieee.org\/Xplorehelp\/downloads\/license-information\/IEEE.html"},{"start":{"date-parts":[[2019,3,1]],"date-time":"2019-03-01T00:00:00Z","timestamp":1551398400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2019,3,1]],"date-time":"2019-03-01T00:00:00Z","timestamp":1551398400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"}],"funder":[{"name":"Herman Berendsen&#x0027;s group"},{"name":"Department of Biophysical Chemistry","award":["Nr 031A300A"],"award-info":[{"award-number":["Nr 031A300A"]}]},{"name":"Department of Biophysical Chemistry"},{"name":"Shanghai Institute of Materia Medica"},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Key R&#x0026;D Program of China","award":["2017YFB0202602","2018YFC0910405","2017YFC1311003","2016YFC1302500","2016YFB0200400","2017YFB0202104"],"award-info":[{"award-number":["2017YFB0202602","2018YFC0910405","2017YFC1311003","2016YFC1302500","2016YFB0200400","2017YFB0202104"]}]},{"DOI":"10.13039\/501100001809","name":"NSFC","doi-asserted-by":"crossref","award":["61772543","U1435222","61625202","61272056"],"award-info":[{"award-number":["61772543","U1435222","61625202","61272056"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Peng Cheng Lab"},{"DOI":"10.13039\/501100011220","name":"State Key Laboratory of Chemo\/Biosensing and Chemometrics","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100011220","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Guangdong Provincial Department of Science and Technology","award":["2016B090918122"],"award-info":[{"award-number":["2016B090918122"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IEEE\/ACM Trans. Comput. Biol. and Bioinf."],"published-print":{"date-parts":[[2019,3,1]]},"DOI":"10.1109\/tcbb.2017.2713362","type":"journal-article","created":{"date-parts":[[2017,6,16]],"date-time":"2017-06-16T18:21:10Z","timestamp":1497637270000},"page":"425-433","source":"Crossref","is-referenced-by-count":10,"title":["A CPU\/MIC Collaborated Parallel Framework for GROMACS on Tianhe-2 Supercomputer"],"prefix":"10.1109","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4647-2615","authenticated-orcid":false,"given":"Shaoliang","family":"Peng","sequence":"first","affiliation":[]},{"given":"Yingbo","family":"Cui","sequence":"additional","affiliation":[]},{"given":"Shunyun","family":"Yang","sequence":"additional","affiliation":[]},{"given":"Wenhe","family":"Su","sequence":"additional","affiliation":[]},{"given":"Xiaoyu","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Tenglilang","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Weiguo","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Xingming","family":"Zhao","sequence":"additional","affiliation":[]}],"member":"263","reference":[{"key":"ref33","doi-asserted-by":"publisher","DOI":"10.1080\/00268978300102851"},{"key":"ref32","article-title":"Visual molecular dynamics[J]","author":"surhone","year":"2010","journal-title":"OS9 Betascript Publishing"},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21766"},{"key":"ref30","first-page":"379","article-title":"Hamiltonian replica-exchange in GROMACS: A flexible implementation","volume":"112","author":"bussi","year":"2013","journal-title":"Molecular Phys Int J Inter Between Chem Phys"},{"key":"ref10","doi-asserted-by":"publisher","DOI":"10.1080\/00268978400101201"},{"key":"ref11","doi-asserted-by":"publisher","DOI":"10.2172\/10176421"},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20291"},{"key":"ref13","first-page":"710","article-title":"GROMACS&#x2014;the road ahead","volume":"1","author":"spoel","year":"2011","journal-title":"Wiley Interdisciplinary Reviews: Computational Molecular Science"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1093\/bioinformatics\/bts020","article-title":"GROMACS molecule liquid database","volume":"28","author":"david","year":"2012","journal-title":"Bioinf"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1093\/bioinformatics\/btt055","article-title":"GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit","volume":"29","author":"van der spoel","year":"2013","journal-title":"Bioinf"},{"key":"ref16","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20703"},{"key":"ref17","article-title":"Intel Xeon Phi coprocessor high performance programming[J]","author":"more","year":"2013","journal-title":"J Comput Sci Technol"},{"key":"ref18","doi-asserted-by":"publisher","DOI":"10.1109\/IPDPS.2014.35"},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.1126\/science.265.5170.361"},{"year":"2014","key":"ref4"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1002\/jcc.21703","article-title":"On easy implementation of a variant of the replica exchange with solute tempering in GROMACS","volume":"32","author":"tsuyoshi","year":"2011","journal-title":"J Comput Chemistry"},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.1063\/1.1743957"},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.1021\/ci400172g"},{"year":"0","key":"ref6"},{"key":"ref29","first-page":"736","article-title":"The GROMACS and NAMD software packages comparison","volume":"1","author":"poghosyan","year":"2006","journal-title":"Commun Comput Phys"},{"key":"ref5","doi-asserted-by":"publisher","DOI":"10.1109\/CCGrid.2015.65"},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.1063\/1.467468"},{"year":"0","key":"ref7"},{"year":"2014","key":"ref2"},{"year":"2015","key":"ref1"},{"key":"ref9","first-page":"1545","article-title":"Improved simulation of liquid water by molecular dynamics","volume":"60","year":"1974","journal-title":"Chemical Phys"},{"key":"ref20","doi-asserted-by":"publisher","DOI":"10.4137\/BBI.S3207"},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.1007\/s008940100045"},{"key":"ref21","doi-asserted-by":"publisher","DOI":"10.1016\/0010-4655(95)00042-E"},{"key":"ref24","doi-asserted-by":"publisher","DOI":"10.1109\/IPDPS.2007.370560"},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.1021\/ct700301q"},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.1021\/ct300102d"},{"key":"ref25","first-page":"1603","article-title":"Research in porting MD simulation software GROMACS on GPGPU based on CUDA","volume":"27","author":"yan","year":"2010","journal-title":"Computers and Applied Chemistry"}],"container-title":["IEEE\/ACM Transactions on Computational Biology and Bioinformatics"],"original-title":[],"link":[{"URL":"http:\/\/xplorestaging.ieee.org\/ielx7\/8857\/8680721\/07950954.pdf?arnumber=7950954","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,13]],"date-time":"2022-07-13T20:53:02Z","timestamp":1657745582000},"score":1,"resource":{"primary":{"URL":"https:\/\/ieeexplore.ieee.org\/document\/7950954\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,3,1]]},"references-count":33,"journal-issue":{"issue":"2"},"URL":"https:\/\/doi.org\/10.1109\/tcbb.2017.2713362","relation":{},"ISSN":["1545-5963","1557-9964","2374-0043"],"issn-type":[{"type":"print","value":"1545-5963"},{"type":"electronic","value":"1557-9964"},{"type":"electronic","value":"2374-0043"}],"subject":[],"published":{"date-parts":[[2019,3,1]]}}}