125811 20241129133040.0 doi 10.1016/j.cpc.2023.108742 sideral 133226 ART-2023-133226 eng López-Villellas, L. Universidad de Zaragoza (orcid)0000-0002-1891-4359 Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code 2023 Access copy available to the general public Unrestricted In molecular dynamics simulations we can often increase the time step by imposing constraints on bond lengths and bond angles. This allows us to extend the length of the time interval and therefore the range of physical phenomena that we can afford to simulate. We examine the existing algorithms and software for solving nonlinear constraint equations in parallel and we explain why it is necessary to advance the state-of-the-art. We present ILVES-PC, a new algorithm for imposing bond constraints on proteins accurately and efficiently. It solves the same system of differential algebraic equations as the celebrated SHAKE algorithm, but ILVES-PC solves the nonlinear constraint equations using Newton’s method rather than the nonlinear Gauss-Seidel method. Moreover, ILVES-PC solves the necessary linear systems using a specialized linear solver that exploits the structure of the protein. ILVES-PC can rapidly solve constraint equations as accurately as the hardware will allow. The run-time of ILVES-PC is proportional to the number of constraints. We have integrated ILVES-PC into GROMACS and simulated proteins of different sizes. Compared with SHAKE, we have achieved speedups of up to 4.9× in single-threaded executions and up to 76× in shared-memory multi-threaded executions. Moreover, ILVES-PC is more accurate than P-LINCS algorithm. Our work is a proof-of-concept of the utility of software designed specifically for the simulation of polymers. info:eu-repo/grantAgreement/ES/AEI/IJCI-2020-045916-I info:eu-repo/grantAgreement/ES/AEI/PID2019-105660RB-C21-AEI-10.13039-501100011033 info:eu-repo/grantAgreement/ES/AEI/RYC-2016-21104 info:eu-repo/grantAgreement/ES/DGA-ESF/T58-20R info:eu-repo/grantAgreement/ES/DGA/E45-20R info:eu-repo/grantAgreement/ES/MICINN/PID2019-107255GB-C21-AEI-10.13039/501100011033 info:eu-repo/grantAgreement/ES/MICINN/PID2019-107293GB-I00 info:eu-repo/semantics/openAccess by-nc-nd http://creativecommons.org/licenses/by-nc-nd/3.0/es/ 7.2 2023 PHYSICS, MATHEMATICAL 1 / 60 = 0.017 2023 Q1 T1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS 16 / 170 = 0.094 2023 Q1 T1 1.79 2023 Physics and Astronomy (miscellaneous) 2023 Q1 Hardware and Architecture 2023 Q1 12.1 2023 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Kjelgaard Mikkelsen C. Ch. Galano-Frutos, J. J. Universidad de Zaragoza (orcid)0000-0002-1896-7805 Marco-Sola, S. Alastruey-Benedé, J. Universidad de Zaragoza (orcid)0000-0003-4164-5078 Ibáñez, P. Universidad de Zaragoza (orcid)0000-0002-5916-7898 Moretó, M. Sancho, J. Universidad de Zaragoza (orcid)0000-0002-2879-9200 García-Risueño, P. 5007 035 Universidad de Zaragoza Dpto. Informát.Ingenie.Sistms. Área Arquit.Tecnología Comput. 1002 060 Universidad de Zaragoza Dpto. Bioq.Biolog.Mol. Celular Área Bioquímica y Biolog.Mole. 288 (2023), 108742 [12 pp.] Comput. phys. commun. COMPUTER PHYSICS COMMUNICATIONS 0010-4655 741521 http://zaguan.unizar.es/record/125811/files/texto_completo.pdf Versión publicada 2625399 http://zaguan.unizar.es/record/125811/files/texto_completo.jpg?subformat=icon icon Versión publicada oai:zaguan.unizar.es:125811 articulos driver 2024-11-29-13:28:56 ARTICLE