Combining stochastic and deterministic approaches within high efficiency molecular simulations

• Autorzy: Bruno Escribano , Elena Akhmatskaya , Jon Mujika
• Języki publikacji: EN

Abstrakty

EN

Generalized 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.

Słowa kluczowe

EN

Hybrid Monte Carlo; Shadow Hamiltonian; Molecular dynamics

Kategorie tematyczne

• 65P10: Hamiltonian systems including symplectic integrators
• 82B80: Numerical methods (Monte Carlo, series resummation, etc.)

• Wydawca: De Gruyter Open
• Czasopismo: Open Mathematics
• Rocznik: 2013
• Tom: 11
• Numer: 4
• Strony: 787-799

Daty

wydano

2013-04-01

online

2013-01-29

Twórcy

autor

Bruno Escribano

• Basque Center for Applied Mathematics

autor

Elena Akhmatskaya

• Basque Center for Applied Mathematics

autor

Jon Mujika

• Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center, PK 1072

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Identyfikatory

DOI

10.2478/s11533-012-0164-x