From predictors and SHAKE toward unified integration scheme for molecular dynamics
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F67985858%3A_____%2F25%3A00617483" target="_blank" >RIV/67985858:_____/25:00617483 - isvavai.cz</a>
Alternative codes found
RIV/60461373:22340/25:43933512
Result on the web
<a href="https://pubs.aip.org/aip/jcp/article/162/8/084103/3337070/From-predictors-and-SHAKE-toward-unified" target="_blank" >https://pubs.aip.org/aip/jcp/article/162/8/084103/3337070/From-predictors-and-SHAKE-toward-unified</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1063/5.0241560" target="_blank" >10.1063/5.0241560</a>
Alternative languages
Result language
angličtina
Original language name
From predictors and SHAKE toward unified integration scheme for molecular dynamics
Original language description
Molecular dynamics (MD) simulations applied to various special tasks such as thermostats, barostats, external volume control, or external magnetic fields often require tailored integration methods, complicating software development. Here, we propose a unified integration scheme for solving the common sets of equations of motion in MD. To achieve this, we adapted the traditional SHAKE method for treating rigid bonds to a predictor–corrector integration scheme and combined it with the existing time-reversible velocity predictor and box predictor. This new approach enables using both the time-honored Verlet method and the recently improved Gear methods. The resulting unified integration scheme was tested on two simple models and two MD systems: SPC/E water and ionic liquid (1-ethyl-3-methylimidazolium tetrafluoridoborate). Trajectories in microcanonical, Nosé–Hoover canonical, and MTK isobaric ensembles were generated. The results for Verlet-based methods were in excellent agreement with those obtained using conventional integration methods. For particular tasks, the use of higher-order methods can be beneficial. Overall, in comparison with standard approaches, our universal scheme provides a significantly simpler route to devising new integrators and maintaining existing simulation software. Furthermore, our family of new integrators can be efficiently deployed in massively parallel MD software.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
<a href="/en/project/GA22-28869S" target="_blank" >GA22-28869S: Formation of droplets in rapid expansions: Between unary, binary, and heterogeneous paths.</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Chemical Physics
ISSN
0021-9606
e-ISSN
1089-7690
Volume of the periodical
162
Issue of the periodical within the volume
8
Country of publishing house
US - UNITED STATES
Number of pages
16
Pages from-to
084103
UT code for WoS article
001468041000005
EID of the result in the Scopus database
2-s2.0-85219082584