{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,8]],"date-time":"2025-04-08T08:04:25Z","timestamp":1744099465731},"reference-count":39,"publisher":"Wiley","issue":"17","license":[{"start":{"date-parts":[[2021,4,13]],"date-time":"2021-04-13T00:00:00Z","timestamp":1618272000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[2021,6,30]]},"abstract":"Abstract<\/jats:title>In the present study, the Divide and Conquer MBAR (DC\u2010MBAR) method is proposed to predict the free energies based on the data sampled by multi\u2010states simulations. For DC\u2010MBAR method, the overlap between any two alchemical states is calculated first and those with sufficient overlap are defined as the adjacent states. Unlike the traditional MBAR method, which calculates the free energy of each state using all the data at once, DC\u2010MBAR focuses on predicting the free energy changes between adjacent states. To estimate the free energy changes accurately, the other states with overlaps with the two adjacent states bigger than the defined threshold are included in the MBAR equation. At a specific threshold, the free energies predicted by DC\u2010MBAR are very close to those calculated by the traditional MABR method. Furthermore, DC\u2010MBAR scheme can reduce both the computation and memory cost. One important characteristic of DC\u2010MBAR method is linear scaling, which means the CPU time with the change of the number of states is a straight\u2010line relation. As the pair\u2010based calculations are mutually independent and parallelizable, all accessible CPU cores on the HPC cluster could be utilized, which makes DC\u2010MBAR strategy more efficient.<\/jats:p>","DOI":"10.1002\/jcc.26533","type":"journal-article","created":{"date-parts":[[2021,4,14]],"date-time":"2021-04-14T07:59:52Z","timestamp":1618387192000},"page":"1204-1211","update-policy":"http:\/\/dx.doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Free energy change estimation: The Divide and Conquer MBAR<\/scp> method"],"prefix":"10.1002","volume":"42","author":[{"ORCID":"http:\/\/orcid.org\/0000-0001-6336-6550","authenticated-orcid":false,"given":"Xiangyu","family":"Jia","sequence":"first","affiliation":[{"name":"Simcere Pharmaceutical Nanjing China"},{"name":"NYU\u2010ECNU Center for Computational Chemistry at NYU Shanghai Shanghai China"}]},{"given":"Hu","family":"Ge","sequence":"additional","affiliation":[{"name":"Simcere Pharmaceutical Nanjing China"}]},{"given":"Ye","family":"Mei","sequence":"additional","affiliation":[{"name":"NYU\u2010ECNU Center for Computational Chemistry at NYU Shanghai Shanghai China"},{"name":"State Key Laboratory of Precision Spectroscopy, School of Physics and Material Science East China Normal University Shanghai China"}]}],"member":"311","published-online":{"date-parts":[[2021,4,13]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.2978177"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.3701175"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.63.1195"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0010-4655(00)00215-0"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0009-2614(00)01215-X"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1021\/ct2003995"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.5013273"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jced.7b00104"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5b00920"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1080\/01621459.1990.10476213"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1080\/10618600.2015.1113975"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.7b00204"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1214\/aoms\/1177730497"},{"key":"e_1_2_7_15_1","unstructured":"M. R.Shirts arXiv e\u2010prints arXiv:1704.00891v42017."},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.4939768"},{"key":"e_1_2_7_17_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpclett.5b01771"},{"key":"e_1_2_7_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0009-2614(99)01123-9"},{"key":"e_1_2_7_19_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.1740409"},{"key":"e_1_2_7_20_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.462133"},{"key":"e_1_2_7_21_1","doi-asserted-by":"publisher","DOI":"10.1080\/01621459.1995.10476590"},{"key":"e_1_2_7_22_1","doi-asserted-by":"publisher","DOI":"10.1209\/0295-5075\/19\/6\/002"},{"key":"e_1_2_7_23_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.8b01010"},{"key":"e_1_2_7_24_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.8b00571"},{"key":"e_1_2_7_25_1","doi-asserted-by":"publisher","DOI":"10.3390\/molecules23102487"},{"key":"e_1_2_7_26_1","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(77)90121-8"},{"key":"e_1_2_7_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(76)90078-4"},{"key":"e_1_2_7_28_1","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.91.140601"},{"key":"e_1_2_7_29_1","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevE.80.031111"},{"key":"e_1_2_7_30_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-015-9840-9"},{"key":"e_1_2_7_31_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.7b00826"},{"key":"e_1_2_7_32_1","doi-asserted-by":"publisher","DOI":"10.1080\/08927022.2018.1475741"},{"key":"e_1_2_7_33_1","doi-asserted-by":"publisher","DOI":"10.1021\/ct050252w"},{"key":"e_1_2_7_34_1","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevE.56.5018"},{"key":"e_1_2_7_35_1","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.78.2690"},{"key":"e_1_2_7_36_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-39420-x"},{"key":"e_1_2_7_37_1","doi-asserted-by":"publisher","DOI":"10.1021\/cr200093j"},{"key":"e_1_2_7_38_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0009-2614(99)00874-X"},{"key":"e_1_2_7_39_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.1591727"},{"key":"e_1_2_7_40_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.1879792"}],"container-title":["Journal of Computational Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcc.26533","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/jcc.26533","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcc.26533","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T21:31:23Z","timestamp":1693603883000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jcc.26533"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,4,13]]},"references-count":39,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2021,6,30]]}},"alternative-id":["10.1002\/jcc.26533"],"URL":"https:\/\/doi.org\/10.1002\/jcc.26533","archive":["Portico"],"relation":{},"ISSN":["0192-8651","1096-987X"],"issn-type":[{"value":"0192-8651","type":"print"},{"value":"1096-987X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,4,13]]},"assertion":[{"value":"2020-09-17","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-03-25","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-04-13","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}