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공공누리This item is licensed Korea Open Government License

Title
A parallel molecular dynamics simulation scheme for a molecular system with bond constraints in NPT ensemble
Author(s)
오광진
Publication Year
2006-02-15
Abstract
Equations of motion based on an atomic group scaling scheme are described for a molecular system with bond constraints. The NPT ensemble extended system method is employed along with a numerical integration scheme using an operator technique. For parallelization of the integration scheme, a domain decomposition scheme is employed based on a group of atoms which share common constraints. This decomposition scheme fits well into the integration scheme and involves no extra inter-processor communication during the SHAKE/RATTLE procedures. An example is given for a solvated protein system containing a total of 23558 atoms on 64 processors.
Journal Title
computer physics communication
Citation Volume
174
ISSN
0010-4655
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Appears in Collections:
7. KISTI 연구성과 > 학술지 발표논문
URI
https://repository.kisti.re.kr/handle/10580/13640
http://www.ndsl.kr/ndsl/search/detail/article/articleSearchResultDetail.do?cn=NART27394454
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