{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,10,27]],"date-time":"2023-10-27T01:37:31Z","timestamp":1698370651963},"reference-count":48,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2004,9,7]],"date-time":"2004-09-07T00:00:00Z","timestamp":1094515200000},"content-version":"vor","delay-in-days":3843,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[1994,3]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>A coarse\u2010grain parallel implementation of the free energy perturbation (FEP) module of the AMBER molecular dynamics program is described and then demonstrated using five different molecular systems. The difference in the free energy of (aqueous) solvation is calculated for two monovalent cations \u0394\u0394<jats:italic>G<\/jats:italic><jats:sub>aq<\/jats:sub>(Li<jats:sup>+<\/jats:sup> \u0394 Cs<jats:sup>+<\/jats:sup>), and for the zero\u2010sum ethane\u2010to\u2010ethane\u2032 perturbation \u0394\u0394<jats:italic>G<\/jats:italic><jats:sub>aq<\/jats:sub>(CH<jats:sub>3<\/jats:sub>\uf8ffmethyl\uf8ff<jats:italic>X<\/jats:italic> \u2192 <jats:italic>X<\/jats:italic>\uf8ffmethyl\uf8ffCH<jats:sub>3<\/jats:sub>), where <jats:italic>X<\/jats:italic> is a ghost methyl. The difference in binding free energy for a docked HIV\u20101 protease inhibitor into its ethylene mimetic is examined by mutating its fifth peptide bond, \u0394<jats:italic>G<\/jats:italic>(CO\uf8ffNH \u2192 CH\uf8feCH). A potassium ion (K<jats:sup>+<\/jats:sup>) is driven outward from the center of mass of ionophore salinomycin (SAL<jats:sup>\u2212<\/jats:sup>) in a potential of mean force calculation \u0394<jats:italic>G<\/jats:italic><jats:sub>MeOH<\/jats:sub>(SAL<jats:sup>\u2212<\/jats:sup> \u00b7 K<jats:sup>+<\/jats:sup>) carried out in methanol solvent. Parallel speedup obtained is linearly proportional to the number of parallel processors applied. Finally, the difference in free energy of solvation of phenol versus benzene, \u0394\u0394<jats:italic>G<\/jats:italic><jats:sub>oct<\/jats:sub>(phenol \u2192 benzene), is determined in water\u2010saturated octanol and then expressed in terms of relative partition coefficients, \u0394 log(<jats:italic>P<\/jats:italic><jats:sub>o\/w<\/jats:sub>). Because no interprocessor communication is required, this approach is scalable and applicable in general for any parallel architecture or network of machines. FEP calculations run on the nCUBE\/2 using 50 or 100 parallel processors were completed in clock times equivalent to or twice as fast as a Cray Y\u2010MP. The difficulty of ensuring adequate system equilibrium when agradual configurational reorientation follows the mutation of the Hamiltonian is discussed and analyzed. The results of a successful protocol for overcoming this equilibration problem are presented. The types of molecular perturbations for which this method is expected to perform most efficiently are described. \u00a9 1994 by John Wiley &amp; Sons, Inc.<\/jats:p>","DOI":"10.1002\/jcc.540150310","type":"journal-article","created":{"date-parts":[[2005,1,2]],"date-time":"2005-01-02T01:01:11Z","timestamp":1104627671000},"page":"351-373","source":"Crossref","is-referenced-by-count":12,"title":["Free energy perturbation calculations on parallel computers: Demonstrations of scalable linear speedup"],"prefix":"10.1002","volume":"15","author":[{"given":"Stephen E.","family":"Debolt","sequence":"first","affiliation":[]},{"given":"David A.","family":"Pearlman","sequence":"additional","affiliation":[]},{"given":"Peter A.","family":"Kollman","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2004,9,7]]},"reference":[{"key":"e_1_2_1_2_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540140307"},{"key":"e_1_2_1_2_3","doi-asserted-by":"publisher","DOI":"10.1007\/BF01113277"},{"key":"e_1_2_1_2_4","doi-asserted-by":"publisher","DOI":"10.1016\/0010-4655(92)90048-4"},{"key":"e_1_2_1_2_5","doi-asserted-by":"publisher","DOI":"10.1016\/0010-4655(91)90097-5"},{"key":"e_1_2_1_2_6","doi-asserted-by":"publisher","DOI":"10.1016\/0167-8191(92)90091-K"},{"key":"e_1_2_1_2_7","doi-asserted-by":"publisher","DOI":"10.1016\/0010-4809(92)90019-7"},{"key":"e_1_2_1_2_8","first-page":"98","volume":"28","author":"Sato H.","year":"1992","journal-title":"Fujitsu Scientific & Tech. J."},{"key":"e_1_2_1_2_9","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540130908"},{"key":"e_1_2_1_2_10","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540121016"},{"key":"e_1_2_1_2_11","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540120206"},{"key":"e_1_2_1_2_12","doi-asserted-by":"publisher","DOI":"10.1016\/0097-8485(90)80049-8"},{"key":"e_1_2_1_2_13","volume-title":"Solving Problems on Concurrent Processors. General Techniques and Regular Problems","author":"Fox G. C.","year":"1988"},{"key":"e_1_2_1_2_14","doi-asserted-by":"publisher","DOI":"10.1080\/08927028708080929"},{"key":"e_1_2_1_2_15","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540060617"},{"key":"e_1_2_1_2_16","unstructured":"(c) Machines such as nCUBE\/3 Intel Paragon Cray T3D Fujitsu AP\u20101000 Kendall Square Research KSR\u20101 and others."},{"key":"e_1_2_1_3_2","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1146\/annurev.bb.18.060189.002243","volume":"18","author":"Beveridge D. L.","year":"1989","journal-title":"Annu. Rev. Biophys. Biphys. Chem."},{"key":"e_1_2_1_4_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540070216"},{"key":"e_1_2_1_4_3","unstructured":"U. C.Singh P. K.Weiner J. W.Caldwell andP. A.Kollman AMBER (UCSF) Version 3.0 Department of Pharmaceutical Chemistry University of California San Francisco 1986."},{"key":"e_1_2_1_5_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.455988"},{"key":"e_1_2_1_6_2","volume-title":"Numerical Recipes","author":"Press W. H.","year":"1989"},{"key":"e_1_2_1_7_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.455654"},{"key":"e_1_2_1_8_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.460608"},{"key":"e_1_2_1_9_2","unstructured":"D. A.Pearlman D. A.Case J. A.Caldwell G. L.Seibel U. C.Singh P.Weiner andP. A.Kollman AMBER 4.0 University of California San Francisco 1991."},{"key":"e_1_2_1_10_2","doi-asserted-by":"publisher","DOI":"10.1080\/00268977700102571"},{"key":"e_1_2_1_10_3","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(77)90098-5"},{"key":"e_1_2_1_10_4","doi-asserted-by":"publisher","DOI":"10.1080\/00268978200100942"},{"key":"e_1_2_1_11_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.448118"},{"key":"e_1_2_1_12_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-94-015-7658-1_21"},{"key":"e_1_2_1_13_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.460608"},{"key":"e_1_2_1_14_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.2548279"},{"key":"e_1_2_1_15_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm00167a003"},{"key":"e_1_2_1_16_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00125504"},{"key":"e_1_2_1_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0040-4039(01)87382-2"},{"key":"e_1_2_1_18_2","first-page":"1283","volume":"27","author":"Pressman B. C.","year":"1968","journal-title":"Federation Proc."},{"key":"e_1_2_1_19_2","doi-asserted-by":"publisher","DOI":"10.7164\/antibiotics.27.814"},{"key":"e_1_2_1_20_2","doi-asserted-by":"publisher","DOI":"10.1021\/j100384a009"},{"key":"e_1_2_1_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/0005-2736(86)90070-2"},{"key":"e_1_2_1_21_3","doi-asserted-by":"publisher","DOI":"10.1002\/bscb.19810900708"},{"key":"e_1_2_1_22_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja00177a010"},{"key":"e_1_2_1_23_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540140207"},{"key":"e_1_2_1_24_2","doi-asserted-by":"publisher","DOI":"10.1021\/j100398a015"},{"key":"e_1_2_1_25_2","unstructured":"S. E.DeBoltandP. A.Kollman submitted JACS (1994)."},{"key":"e_1_2_1_26_2","volume-title":"Metal Ions in Solution","author":"Burgess M. A.","year":"1978"},{"key":"e_1_2_1_27_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.456845"},{"key":"e_1_2_1_28_2","unstructured":"C. I.BaylyandP. A.Kollman J. Amer. Chem. Soc. in press (1994)."},{"key":"e_1_2_1_29_2","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(88)80054-7"},{"key":"e_1_2_1_30_2","doi-asserted-by":"publisher","DOI":"10.1016\/0005-2736(86)90070-2"},{"key":"e_1_2_1_31_2","volume-title":"Substituent Constants for Correlation Analysis in Chemistry and Biology","author":"Hansch C.","year":"1979"}],"container-title":["Journal of Computational Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fjcc.540150310","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcc.540150310","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,8]],"date-time":"2023-10-08T04:40:05Z","timestamp":1696740005000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jcc.540150310"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[1994,3]]},"references-count":48,"journal-issue":{"issue":"3","published-print":{"date-parts":[[1994,3]]}},"alternative-id":["10.1002\/jcc.540150310"],"URL":"https:\/\/doi.org\/10.1002\/jcc.540150310","archive":["Portico"],"relation":{},"ISSN":["0192-8651","1096-987X"],"issn-type":[{"value":"0192-8651","type":"print"},{"value":"1096-987X","type":"electronic"}],"subject":[],"published":{"date-parts":[[1994,3]]}}}