ILVES: Accurate and Efficient Bond Length and Angle Constraints in Molecular Dynamics

All-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 cos...

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Autores: López-Villellas, Lorién, Mikkelsen, Carl Christian Kjelgaard, Galano-Frutos, Juan José, Marco-Sola, Santiago, Alastruey-Benedé, Jesús, Ibáñez, Pablo, Echenique, Pablo, Moretó, Miquel, De Rosa, Maria Cristina, García-Risueño, Pablo
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Recursos:Universidad de Zaragoza
Repositorio:Zaguán. Repositorio Digital de la Universidad de Zaragoza
OAI Identifier:oai:zaguan.unizar.es:162809
Acesso em linha:http://zaguan.unizar.es/record/162809
Access Level:acceso abierto
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spelling ILVES: Accurate and Efficient Bond Length and Angle Constraints in Molecular DynamicsLópez-Villellas, LoriénMikkelsen, Carl Christian KjelgaardGalano-Frutos, Juan JoséMarco-Sola, SantiagoAlastruey-Benedé, JesúsIbáñez, PabloEchenique, PabloMoretó, MiquelDe Rosa, Maria CristinaGarcía-Risueño, PabloAll-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.2025info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://zaguan.unizar.es/record/162809reponame:Zaguán. Repositorio Digital de la Universidad de Zaragozainstname:Universidad de ZaragozaInglésinfo:eu-repo/grantAgreement/ES/DGA/E45-20Rinfo:eu-repo/grantAgreement/ES/DGA/T58-23Rinfo:eu-repo/grantAgreement/ES/MICINN/PID2022-136454NB-C22info:eu-repo/semantics/openAccessoai:zaguan.unizar.es:1628092026-05-29T13:59:51Z
dc.title.none.fl_str_mv ILVES: Accurate and Efficient Bond Length and Angle Constraints in Molecular Dynamics
title ILVES: Accurate and Efficient Bond Length and Angle Constraints in Molecular Dynamics
spellingShingle ILVES: Accurate and Efficient Bond Length and Angle Constraints in Molecular Dynamics
López-Villellas, Lorién
title_short ILVES: Accurate and Efficient Bond Length and Angle Constraints in Molecular Dynamics
title_full ILVES: Accurate and Efficient Bond Length and Angle Constraints in Molecular Dynamics
title_fullStr ILVES: Accurate and Efficient Bond Length and Angle Constraints in Molecular Dynamics
title_full_unstemmed ILVES: Accurate and Efficient Bond Length and Angle Constraints in Molecular Dynamics
title_sort ILVES: Accurate and Efficient Bond Length and Angle Constraints in Molecular Dynamics
dc.creator.none.fl_str_mv López-Villellas, Lorién
Mikkelsen, Carl Christian Kjelgaard
Galano-Frutos, Juan José
Marco-Sola, Santiago
Alastruey-Benedé, Jesús
Ibáñez, Pablo
Echenique, Pablo
Moretó, Miquel
De Rosa, Maria Cristina
García-Risueño, Pablo
author López-Villellas, Lorién
author_facet López-Villellas, Lorién
Mikkelsen, Carl Christian Kjelgaard
Galano-Frutos, Juan José
Marco-Sola, Santiago
Alastruey-Benedé, Jesús
Ibáñez, Pablo
Echenique, Pablo
Moretó, Miquel
De Rosa, Maria Cristina
García-Risueño, Pablo
author_role author
author2 Mikkelsen, Carl Christian Kjelgaard
Galano-Frutos, Juan José
Marco-Sola, Santiago
Alastruey-Benedé, Jesús
Ibáñez, Pablo
Echenique, Pablo
Moretó, Miquel
De Rosa, Maria Cristina
García-Risueño, Pablo
author2_role author
author
author
author
author
author
author
author
author
description All-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.
publishDate 2025
dc.date.none.fl_str_mv 2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
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dc.identifier.none.fl_str_mv http://zaguan.unizar.es/record/162809
url http://zaguan.unizar.es/record/162809
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv info:eu-repo/grantAgreement/ES/DGA/E45-20R
info:eu-repo/grantAgreement/ES/DGA/T58-23R
info:eu-repo/grantAgreement/ES/MICINN/PID2022-136454NB-C22
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
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dc.source.none.fl_str_mv reponame:Zaguán. Repositorio Digital de la Universidad de Zaragoza
instname:Universidad de Zaragoza
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