000125811 001__ 125811
000125811 005__ 20241129133040.0
000125811 0247_ $$2doi$$a10.1016/j.cpc.2023.108742
000125811 0248_ $$2sideral$$a133226
000125811 037__ $$aART-2023-133226
000125811 041__ $$aeng
000125811 100__ $$0(orcid)0000-0002-1891-4359$$aLópez-Villellas, L.$$uUniversidad de Zaragoza
000125811 245__ $$aAccurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code
000125811 260__ $$c2023
000125811 5060_ $$aAccess copy available to the general public$$fUnrestricted
000125811 5203_ $$aIn 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.
000125811 536__ $$9info:eu-repo/grantAgreement/ES/DGA/E45-20R$$9info:eu-repo/grantAgreement/ES/DGA-ESF/T58-20R$$9info:eu-repo/grantAgreement/ES/AEI/RYC-2016-21104$$9info:eu-repo/grantAgreement/ES/AEI/PID2019-105660RB-C21-AEI-10.13039-501100011033$$9info:eu-repo/grantAgreement/ES/AEI/IJCI-2020-045916-I$$9info:eu-repo/grantAgreement/ES/MICINN/PID2019-107255GB-C21-AEI-10.13039/501100011033$$9info:eu-repo/grantAgreement/ES/MICINN/PID2019-107293GB-I00
000125811 540__ $$9info:eu-repo/semantics/openAccess$$aby-nc-nd$$uhttp://creativecommons.org/licenses/by-nc-nd/3.0/es/
000125811 590__ $$a7.2$$b2023
000125811 592__ $$a1.79$$b2023
000125811 591__ $$aPHYSICS, MATHEMATICAL$$b1 / 60 = 0.017$$c2023$$dQ1$$eT1
000125811 593__ $$aPhysics and Astronomy (miscellaneous)$$c2023$$dQ1
000125811 591__ $$aCOMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS$$b16 / 170 = 0.094$$c2023$$dQ1$$eT1
000125811 593__ $$aHardware and Architecture$$c2023$$dQ1
000125811 594__ $$a12.1$$b2023
000125811 655_4 $$ainfo:eu-repo/semantics/article$$vinfo:eu-repo/semantics/publishedVersion
000125811 700__ $$aKjelgaard Mikkelsen C. Ch.
000125811 700__ $$0(orcid)0000-0002-1896-7805$$aGalano-Frutos, J. J.$$uUniversidad de Zaragoza
000125811 700__ $$aMarco-Sola, S.
000125811 700__ $$0(orcid)0000-0003-4164-5078$$aAlastruey-Benedé, J.$$uUniversidad de Zaragoza
000125811 700__ $$0(orcid)0000-0002-5916-7898$$aIbáñez, P.$$uUniversidad de Zaragoza
000125811 700__ $$aMoretó, M.
000125811 700__ $$0(orcid)0000-0002-2879-9200$$aSancho, J.$$uUniversidad de Zaragoza
000125811 700__ $$aGarcía-Risueño, P.
000125811 7102_ $$15007$$2035$$aUniversidad de Zaragoza$$bDpto. Informát.Ingenie.Sistms.$$cÁrea Arquit.Tecnología Comput.
000125811 7102_ $$11002$$2060$$aUniversidad de Zaragoza$$bDpto. Bioq.Biolog.Mol. Celular$$cÁrea Bioquímica y Biolog.Mole.
000125811 773__ $$g288 (2023), 108742 [12 pp.]$$pComput. phys. commun.$$tCOMPUTER PHYSICS COMMUNICATIONS$$x0010-4655
000125811 8564_ $$s741521$$uhttps://zaguan.unizar.es/record/125811/files/texto_completo.pdf$$yVersión publicada
000125811 8564_ $$s2625399$$uhttps://zaguan.unizar.es/record/125811/files/texto_completo.jpg?subformat=icon$$xicon$$yVersión publicada
000125811 909CO $$ooai:zaguan.unizar.es:125811$$particulos$$pdriver
000125811 951__ $$a2024-11-29-13:28:56
000125811 980__ $$aARTICLE