{"title":"直角坐标系下半刚性分子动力学的SHAKE和精确约束满足，1973-1977","authors":"Daniele Macuglia","doi":"10.1007/s00407-023-00306-0","DOIUrl":null,"url":null,"abstract":"<div><p>This essay traces the history of early molecular dynamics simulations, specifically exploring the development of SHAKE, a constraint-based technique devised in 1976 by Jean-Paul Ryckaert, Giovanni Ciccotti and the late Herman Berendsen at CECAM (Centre Européen de Calcul Atomique et Moléculaire). The work of the three scientists proved to be instrumental in giving impetus to the MD simulation of complex polymer systems and it currently underpins the work of thousands of researchers worldwide who are engaged in computational physics, chemistry and biology. Despite its impact and its role in bringing different scientific fields together, accurate historical studies on the birth of SHAKE are virtually absent. By collecting and elaborating on the accounts of Ryckaert and Ciccotti, this essay aims to fill this gap, while also commenting on the conceptual and computational difficulties faced by its developers.</p></div>","PeriodicalId":50982,"journal":{"name":"Archive for History of Exact Sciences","volume":"77 4","pages":"345 - 371"},"PeriodicalIF":0.7000,"publicationDate":"2023-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00407-023-00306-0.pdf","citationCount":"0","resultStr":"{\"title\":\"SHAKE and the exact constraint satisfaction of the dynamics of semi-rigid molecules in Cartesian coordinates, 1973–1977\",\"authors\":\"Daniele Macuglia\",\"doi\":\"10.1007/s00407-023-00306-0\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>This essay traces the history of early molecular dynamics simulations, specifically exploring the development of SHAKE, a constraint-based technique devised in 1976 by Jean-Paul Ryckaert, Giovanni Ciccotti and the late Herman Berendsen at CECAM (Centre Européen de Calcul Atomique et Moléculaire). The work of the three scientists proved to be instrumental in giving impetus to the MD simulation of complex polymer systems and it currently underpins the work of thousands of researchers worldwide who are engaged in computational physics, chemistry and biology. Despite its impact and its role in bringing different scientific fields together, accurate historical studies on the birth of SHAKE are virtually absent. By collecting and elaborating on the accounts of Ryckaert and Ciccotti, this essay aims to fill this gap, while also commenting on the conceptual and computational difficulties faced by its developers.</p></div>\",\"PeriodicalId\":50982,\"journal\":{\"name\":\"Archive for History of Exact Sciences\",\"volume\":\"77 4\",\"pages\":\"345 - 371\"},\"PeriodicalIF\":0.7000,\"publicationDate\":\"2023-02-21\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://link.springer.com/content/pdf/10.1007/s00407-023-00306-0.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Archive for History of Exact Sciences\",\"FirstCategoryId\":\"98\",\"ListUrlMain\":\"https://link.springer.com/article/10.1007/s00407-023-00306-0\",\"RegionNum\":2,\"RegionCategory\":\"哲学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"HISTORY & PHILOSOPHY OF SCIENCE\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Archive for History of Exact Sciences","FirstCategoryId":"98","ListUrlMain":"https://link.springer.com/article/10.1007/s00407-023-00306-0","RegionNum":2,"RegionCategory":"哲学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"HISTORY & PHILOSOPHY OF SCIENCE","Score":null,"Total":0}
SHAKE and the exact constraint satisfaction of the dynamics of semi-rigid molecules in Cartesian coordinates, 1973–1977
This essay traces the history of early molecular dynamics simulations, specifically exploring the development of SHAKE, a constraint-based technique devised in 1976 by Jean-Paul Ryckaert, Giovanni Ciccotti and the late Herman Berendsen at CECAM (Centre Européen de Calcul Atomique et Moléculaire). The work of the three scientists proved to be instrumental in giving impetus to the MD simulation of complex polymer systems and it currently underpins the work of thousands of researchers worldwide who are engaged in computational physics, chemistry and biology. Despite its impact and its role in bringing different scientific fields together, accurate historical studies on the birth of SHAKE are virtually absent. By collecting and elaborating on the accounts of Ryckaert and Ciccotti, this essay aims to fill this gap, while also commenting on the conceptual and computational difficulties faced by its developers.
期刊介绍：
The Archive for History of Exact Sciences casts light upon the conceptual groundwork of the sciences by analyzing the historical course of rigorous quantitative thought and the precise theory of nature in the fields of mathematics, physics, technical chemistry, computer science, astronomy, and the biological sciences, embracing as well their connections to experiment. This journal nourishes historical research meeting the standards of the mathematical sciences. Its aim is to give rapid and full publication to writings of exceptional depth, scope, and permanence.
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