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2013 | 11 | 4 | 787-799
Tytuł artykułu

Combining stochastic and deterministic approaches within high efficiency molecular simulations

Treść / Zawartość
Warianty tytułu
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.
Wydawca
Czasopismo
Rocznik
Tom
11
Numer
4
Strony
787-799
Opis fizyczny
Daty
wydano
2013-04-01
online
2013-01-29
Twórcy
autor
  • Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center, PK 1072
Bibliografia
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  • [3] Akhmatskaya E., Bou-Rabee N., Reich S., Erratum to ”A comparison of generalized hybrid Monte Carlo methods with and without momentum flip” [J. Comput. Phys. 228 (2009) 2256–2265], J. Comput. Phys., 2009, 228(19), 7492–7496 http://dx.doi.org/10.1016/j.jcp.2009.06.039
  • [4] Akhmatskaya E., Reich S., GSHMC: An efficient method for molecular simulation, J. Comput. Phys., 2008, 227(10), 4934–4954 http://dx.doi.org/10.1016/j.jcp.2008.01.023
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  • [21] Mujika J.I., Escribano B., Akhmatskaya E., Ugalde J.M., Lopez X., Molecular dynamics simulations of iron- and aluminum-loaded serum transferrin: protonation of Tyr188 is necessary to prompt the metal release, Biochemistry, 2012, 51(35), 7017–7027 http://dx.doi.org/10.1021/bi300584p
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  • [25] Wee C.L., Sansom M.S., Reich S., Akhmatskaya E., Improved sampling for simulations of interfacial membrane proteins: application of generalized shadow hybrid Monte Carlo to a peptide toxin/bilayer system, The Journal of Physical Chemistry B, 2008, 112(18), 5710–5717 http://dx.doi.org/10.1021/jp076712u
  • [26] GROMACS Programmer’s Guide, available at http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmer
Typ dokumentu
Bibliografia
Identyfikatory
Identyfikator YADDA
bwmeta1.element.doi-10_2478_s11533-012-0164-x
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