{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,31]],"date-time":"2024-05-31T05:59:59Z","timestamp":1717135199674},"reference-count":20,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2008,6,4]],"date-time":"2008-06-04T00:00:00Z","timestamp":1212537600000},"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":[[2009,1,15]]},"abstract":"Abstract<\/jats:title>We describe the application of a special purpose board for molecular dynamics simulations, named MDGRAPE\u20103, to the problem of simulating periodic bio\u2010molecular systems. MDGRAPE\u20103 is the latest board in a series of hardware accelerators designed to calculate the nonbonding long\u2010range interactions much more rapidly than normal processors. So far, MDGRAPEs were mainly applied to isolated systems, where very many nonbonded interactions were calculated without any distance cutoff. However, in order to regulate the density and pressure during simulations of membrane embedded protein systems, one has to evaluate interactions under periodic boundary conditions. For this purpose, we implemented the Particle\u2013Mesh Ewald (PME) method, and its approximation with distance cutoffs and charge neutrality as proposed by Wolf et al., using MDGRAPE\u20103. When the two methods were applied to simulations of two periodic biomolecular systems, a single MDGRAPE\u20103 achieved 30\u201340 times faster computation times than a single conventional processor did in the both cases. Both methods are shown to have the same molecular structures and dynamics of the systems. \u00a9 2008 Wiley Periodicals, Inc. J Comput Chem 2009<\/jats:p>","DOI":"10.1002\/jcc.21035","type":"journal-article","created":{"date-parts":[[2008,6,4]],"date-time":"2008-06-04T11:46:32Z","timestamp":1212579992000},"page":"110-118","source":"Crossref","is-referenced-by-count":42,"title":["Application of MDGRAPE\u20103, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems"],"prefix":"10.1002","volume":"30","author":[{"given":"Gota","family":"Kikugawa","sequence":"first","affiliation":[]},{"given":"Rossen","family":"Apostolov","sequence":"additional","affiliation":[]},{"given":"Narutoshi","family":"Kamiya","sequence":"additional","affiliation":[]},{"given":"Makoto","family":"Taiji","sequence":"additional","affiliation":[]},{"given":"Ryutaro","family":"Himeno","sequence":"additional","affiliation":[]},{"given":"Haruki","family":"Nakamura","sequence":"additional","affiliation":[]},{"given":"Yasushige","family":"Yonezawa","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2008,6,4]]},"reference":[{"key":"e_1_2_6_2_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja00124a002"},{"key":"e_1_2_6_3_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540040211"},{"key":"e_1_2_6_4_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.283.5401.501"},{"key":"e_1_2_6_5_2","series-title":"NIC Workshop: From Computational Biophysics to Systems Biology 2006, NIC Series","first-page":"29","author":"Narumi T.","year":"2006"},{"key":"e_1_2_6_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0010-4655(03)00349-7"},{"key":"e_1_2_6_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0009-2614(99)00400-5"},{"key":"e_1_2_6_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cplett.2005.02.073"},{"key":"e_1_2_6_9_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.463935"},{"key":"e_1_2_6_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/0009-2614(92)90053-P"},{"key":"e_1_2_6_11_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540150702"},{"key":"e_1_2_6_12_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.464397"},{"key":"e_1_2_6_13_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.478738"},{"key":"e_1_2_6_14_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.1364638"},{"key":"e_1_2_6_15_2","doi-asserted-by":"publisher","DOI":"10.1021\/jp025949h"},{"key":"e_1_2_6_16_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.1858860"},{"key":"e_1_2_6_17_2","doi-asserted-by":"publisher","DOI":"10.1080\/00268970600551155"},{"key":"e_1_2_6_18_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.2206581"},{"key":"e_1_2_6_19_2","doi-asserted-by":"publisher","DOI":"10.1021\/jp035478e"},{"key":"e_1_2_6_20_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.445869"},{"key":"e_1_2_6_21_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.470117"}],"container-title":["Journal of Computational Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fjcc.21035","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcc.21035","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,29]],"date-time":"2023-09-29T04:46:07Z","timestamp":1695962767000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jcc.21035"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,6,4]]},"references-count":20,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,1,15]]}},"alternative-id":["10.1002\/jcc.21035"],"URL":"https:\/\/doi.org\/10.1002\/jcc.21035","archive":["Portico"],"relation":{},"ISSN":["0192-8651","1096-987X"],"issn-type":[{"value":"0192-8651","type":"print"},{"value":"1096-987X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,6,4]]}}}