{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,1]],"date-time":"2025-05-01T18:25:18Z","timestamp":1746123918351},"reference-count":62,"publisher":"Wiley","issue":"11","license":[{"start":{"date-parts":[[2009,5,6]],"date-time":"2009-05-06T00:00:00Z","timestamp":1241568000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[2009,8]]},"abstract":"Abstract<\/jats:title>Metadynamics is a widely used and successful method for reconstructing the free\u2010energy surface of complex systems as a function of a small number of suitably chosen collective variables. This is achieved by biasing the dynamics of the system. The bias acting on the collective variables distorts the probability distribution of the other variables. Here we present a simple reweighting algorithm for recovering the unbiased probability distribution of any variable from a well\u2010tempered metadynamics simulation. We show the efficiency of the reweighting procedure by reconstructing the distribution of the four backbone dihedral angles of alanine dipeptide from two and even one dimensional metadynamics simulation. \u00a9 2009 Wiley Periodicals, Inc. J Comput Chem 2009<\/jats:p>","DOI":"10.1002\/jcc.21305","type":"journal-article","created":{"date-parts":[[2009,5,6]],"date-time":"2009-05-06T13:08:51Z","timestamp":1241615331000},"page":"1615-1621","source":"Crossref","is-referenced-by-count":306,"title":["Reconstructing the equilibrium Boltzmann distribution from well\u2010tempered metadynamics"],"prefix":"10.1002","volume":"30","author":[{"given":"M.","family":"Bonomi","sequence":"first","affiliation":[]},{"given":"A.","family":"Barducci","sequence":"additional","affiliation":[]},{"given":"M.","family":"Parrinello","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2009,5,6]]},"reference":[{"key":"e_1_2_6_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0009-2614(97)01198-6"},{"key":"e_1_2_6_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0009-2614(99)01123-9"},{"key":"e_1_2_6_4_2","doi-asserted-by":"publisher","DOI":"10.1209\/0295-5075\/19\/6\/002"},{"key":"e_1_2_6_5_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0506346102"},{"key":"e_1_2_6_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0009-2614(97)01074-9"},{"key":"e_1_2_6_7_2","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.86.2050"},{"key":"e_1_2_6_8_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.1323224"},{"key":"e_1_2_6_9_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.475562"},{"key":"e_1_2_6_10_2","first-page":"20","volume":"54","author":"Bolhuis P. G.","year":"2002","journal-title":"Ann Rev Phys Chem"},{"key":"e_1_2_6_11_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.1562614"},{"key":"e_1_2_6_12_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.1738640"},{"key":"e_1_2_6_13_2","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.94.018104"},{"key":"e_1_2_6_14_2","doi-asserted-by":"publisher","DOI":"10.1021\/jp0455430"},{"key":"e_1_2_6_15_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.2212942"},{"key":"e_1_2_6_16_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.431685"},{"key":"e_1_2_6_17_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.3810157"},{"key":"e_1_2_6_18_2","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.61.2635"},{"key":"e_1_2_6_19_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00124016"},{"key":"e_1_2_6_20_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540161104"},{"key":"e_1_2_6_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/0010-4655(95)00053-I"},{"key":"e_1_2_6_22_2","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevE.52.2893"},{"key":"e_1_2_6_23_2","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.78.3908"},{"key":"e_1_2_6_24_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.1410978"},{"key":"e_1_2_6_25_2","doi-asserted-by":"publisher","DOI":"10.1021\/jp062755j"},{"key":"e_1_2_6_26_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.202427399"},{"key":"e_1_2_6_27_2","first-page":"489","volume":"220","author":"Martonak R.","year":"2005","journal-title":"Kristallogr"},{"key":"e_1_2_6_28_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0408094102"},{"key":"e_1_2_6_29_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature04439"},{"key":"e_1_2_6_30_2","doi-asserted-by":"publisher","DOI":"10.1021\/jp055809i"},{"key":"e_1_2_6_31_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja057076l"},{"key":"e_1_2_6_32_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja063295a"},{"key":"e_1_2_6_33_2","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.96.095502"},{"key":"e_1_2_6_34_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.2741552"},{"key":"e_1_2_6_35_2","doi-asserted-by":"publisher","DOI":"10.1021\/jp068587c"},{"key":"e_1_2_6_36_2","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.100.185501"},{"key":"e_1_2_6_37_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.2888999"},{"key":"e_1_2_6_38_2","doi-asserted-by":"crossref","first-page":"114707","DOI":"10.1063\/1.2841081","volume":"128","author":"Prestipino S.","year":"2008","journal-title":"J Chem Phys"},{"key":"e_1_2_6_39_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn561"},{"key":"e_1_2_6_40_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja803652f"},{"key":"e_1_2_6_41_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja806846q"},{"key":"e_1_2_6_42_2","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.96.090601"},{"key":"e_1_2_6_43_2","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1142\/9781848162013_0011","volume-title":"Physical Biology","author":"Parrinello M.","year":"2008"},{"key":"e_1_2_6_44_2","doi-asserted-by":"publisher","DOI":"10.1088\/0034-4885\/71\/12\/126601"},{"key":"e_1_2_6_45_2","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1140\/epjb\/e2008-00232-8","volume":"63","author":"Tiana G.","year":"2008","journal-title":"Eur Phys J B"},{"key":"e_1_2_6_46_2","doi-asserted-by":"publisher","DOI":"10.1021\/jp054359r"},{"key":"e_1_2_6_47_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja062463w"},{"key":"e_1_2_6_48_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.21852"},{"key":"e_1_2_6_49_2","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.100.020603"},{"key":"e_1_2_6_50_2","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(77)90121-8"},{"key":"e_1_2_6_51_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.100127697"},{"key":"e_1_2_6_52_2","doi-asserted-by":"publisher","DOI":"10.1021\/jp045546c"},{"key":"e_1_2_6_53_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.1571817"},{"key":"e_1_2_6_54_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.2829861"},{"key":"e_1_2_6_55_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.2432340"},{"key":"e_1_2_6_56_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.461335"},{"key":"e_1_2_6_57_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1450::AID-JCC3>3.0.CO;2-I"},{"key":"e_1_2_6_58_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.477819"},{"key":"e_1_2_6_59_2","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(96)00018-5"},{"key":"e_1_2_6_60_2","doi-asserted-by":"publisher","DOI":"10.1021\/jp973084f"},{"key":"e_1_2_6_61_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20289"},{"key":"e_1_2_6_62_2","doi-asserted-by":"publisher","DOI":"10.1021\/jp045424k"},{"key":"e_1_2_6_63_2","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.92.170601"}],"container-title":["Journal of Computational Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fjcc.21305","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcc.21305","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,12]],"date-time":"2023-09-12T07:47:33Z","timestamp":1694504853000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jcc.21305"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,5,6]]},"references-count":62,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2009,8]]}},"alternative-id":["10.1002\/jcc.21305"],"URL":"https:\/\/doi.org\/10.1002\/jcc.21305","archive":["Portico"],"relation":{},"ISSN":["0192-8651","1096-987X"],"issn-type":[{"value":"0192-8651","type":"print"},{"value":"1096-987X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,5,6]]}}}