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dc.contributor.authorEscribano, B.
dc.contributor.authorAkhmatskaya, E. 
dc.contributor.authorMujika, J.I.
dc.date.accessioned2017-02-21T08:16:49Z
dc.date.available2017-02-21T08:16:49Z
dc.date.issued2013-12-31
dc.identifier.issn1895-1074
dc.identifier.urihttp://hdl.handle.net/20.500.11824/437
dc.description.abstractGeneralized Shadow Hybrid Monte Carlo (GSHMC) is a method for molecular simulations that rigorously alternates Monte Carlo sampling from a canonical ensemble with integration of trajectories using Molecular Dynamics (MD). While conventional hybrid Monte Carlo methods completely re-sample particle's velocities between MD trajectories, our method suggests a partial velocity update procedure which keeps a part of the dynamic information throughout the simulation. We use shadow (modified) Hamiltonians, the asymptotic expansions in powers of the discretization parameter corresponding to timestep, which are conserved by symplectic integrators to higher accuracy than true Hamiltonians. We present the implementation of this method into the highly efficient MD code GROMACS and demonstrate its performance and accuracy on computationally expensive systems like proteins in comparison with the molecular dynamics techniques already available in GROMACS. We take advantage of the state-of-the-art algorithms adopted in the code, leading to an optimal implementation of the method. Our implementation introduces virtually no overhead and can accurately recreate complex biological processes, including rare event dynamics, saving much computational time compared with the conventional simulation methods.
dc.formatapplication/pdf
dc.language.isoengen_US
dc.rightsReconocimiento-NoComercial-CompartirIgual 3.0 Españaen_US
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/3.0/es/en_US
dc.subjectHybrid Monte Carlo
dc.subjectMolecular dynamics
dc.subjectShadow Hamiltonian
dc.titleCombining stochastic and deterministic approaches within high efficiency molecular simulations
dc.typeinfo:eu-repo/semantics/articleen_US
dc.identifier.doi10.2478/s11533-012-0164-x
dc.relation.publisherversionhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-84873209375&doi=10.2478%2fs11533-012-0164-x&partnerID=40&md5=a79c02caead1fc4b0e69060a84000661
dc.rights.accessRightsinfo:eu-repo/semantics/openAccessen_US
dc.type.hasVersioninfo:eu-repo/semantics/publishedVersionen_US
dc.journal.titleCentral European Journal of Mathematicsen_US


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