From predictors and SHAKE toward unified integration scheme for molecular dynamics

Kód výsledku v 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>

Nalezeny alternativní kódy

RIV/60461373:22340/25:43933512

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

From predictors and SHAKE toward unified integration scheme for molecular dynamics

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

From predictors and SHAKE toward unified integration scheme for molecular dynamics

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10403 - Physical chemistry

Projekt

<a href="/cs/project/GA22-28869S" target="_blank" >GA22-28869S: Vznik kapek při rychlých expanzích: přechodné případy mezi unární, binární a hetorogenní cestou</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2025

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Chemical Physics

ISSN

0021-9606

e-ISSN

1089-7690

Svazek periodika

162

Číslo periodika v rámci svazku

8

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

16

Strana od-do

084103

Kód UT WoS článku

001468041000005

EID výsledku v databázi Scopus

2-s2.0-85219082584