000162809 001__ 162809
000162809 005__ 20251017144643.0
000162809 0247_ $$2doi$$a10.1021/acs.jctc.5c01376
000162809 0248_ $$2sideral$$a145338
000162809 037__ $$aART-2025-145338
000162809 041__ $$aeng
000162809 100__ $$0(orcid)0000-0002-1891-4359$$aLópez-Villellas, Lorién$$uUniversidad de Zaragoza
000162809 245__ $$aILVES: Accurate and Efficient Bond Length and Angle Constraints in Molecular Dynamics
000162809 260__ $$c2025
000162809 5060_ $$aAccess copy available to the general public$$fUnrestricted
000162809 5203_ $$aAll-atom, force field-based molecular dynamics simulations are essential tools in computational chemistry, enabling the prediction and analysis of biomolecular systems with atomic-level resolution. However, as system sizes and simulation time scales increase, so does the associated computational cost. To extend simulated time using the same resources, a common strategy is to constrain the fastest degrees of freedom, such as bond lengths, allowing for larger integration time steps without compromising accuracy. The de facto state-of-the-art algorithms for this purpose─SHAKE, LINCS, and P-LINCS─are integrated into most molecular dynamics packages and widely adopted across the field. Despite their impact, these methods exhibit limitations: all converge slowly when high numerical accuracy is required, and the LINCS and P-LINCS algorithms cannot handle general angular constraints, limiting further increases in time step. In this article, we introduce ILVES, a family of parallel algorithms that converge so rapidly that it is now practical to solve bond length and associated angular constraint equations as accurately as the hardware will allow. We have integrated ILVES into Gromacs, and our analysis demonstrates that it is superior to the state-of-the-art when constraining bond lengths. Due to its better convergence properties, we also show that if the time step is increased up to 3.5 fs by enforcing angular constraints, ILVES enables a 1.65× increase in simulated time using the same computational resources and wall-clock time, an outcome unattainable with current methods. This advance can significantly reduce the computational cost of most all-atom molecular dynamics simulations while improving their accuracy and extending access to larger systems and longer time scales.
000162809 536__ $$9info:eu-repo/grantAgreement/ES/DGA/E45-20R$$9info:eu-repo/grantAgreement/ES/DGA/T58-23R$$9info:eu-repo/grantAgreement/ES/MICINN/PID2022-136454NB-C22
000162809 540__ $$9info:eu-repo/semantics/openAccess$$aby$$uhttps://creativecommons.org/licenses/by/4.0/deed.es
000162809 655_4 $$ainfo:eu-repo/semantics/article$$vinfo:eu-repo/semantics/publishedVersion
000162809 700__ $$aMikkelsen, Carl Christian Kjelgaard
000162809 700__ $$0(orcid)0000-0002-1896-7805$$aGalano-Frutos, Juan José
000162809 700__ $$aMarco-Sola, Santiago
000162809 700__ $$0(orcid)0000-0003-4164-5078$$aAlastruey-Benedé, Jesús$$uUniversidad de Zaragoza
000162809 700__ $$0(orcid)0000-0002-5916-7898$$aIbáñez, Pablo$$uUniversidad de Zaragoza
000162809 700__ $$aEchenique, Pablo
000162809 700__ $$aMoretó, Miquel
000162809 700__ $$aDe Rosa, Maria Cristina
000162809 700__ $$aGarcía-Risueño, Pablo
000162809 7102_ $$15007$$2035$$aUniversidad de Zaragoza$$bDpto. Informát.Ingenie.Sistms.$$cÁrea Arquit.Tecnología Comput.
000162809 773__ $$g(2025), [9 pp.]$$pJ. Chem. Theory Comput.$$tJournal of Chemical Theory and Computation$$x1549-9618
000162809 8564_ $$s2609954$$uhttps://zaguan.unizar.es/record/162809/files/texto_completo.pdf$$yVersión publicada
000162809 8564_ $$s2931244$$uhttps://zaguan.unizar.es/record/162809/files/texto_completo.jpg?subformat=icon$$xicon$$yVersión publicada
000162809 909CO $$ooai:zaguan.unizar.es:162809$$particulos$$pdriver
000162809 951__ $$a2025-10-17-14:33:05
000162809 980__ $$aARTICLE