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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

  • Basque Center for Applied Mathematics
  • Basque Center for Applied Mathematics
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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  • [19] MacGillivray R.T., Moore S.A., Chen J., Anderson B.F., Baker H., Luo Y., Bewley M., Smith C.A., Murphy M.E., Wang Y., Mason A.B., Woodworth R.C., Brayer G.D., Baker E.N., Two high-resolution crystal structures of the recombinant N-lobe of human transferrin reveal a structural change implicated in iron release, Biochemistry, 1998, 37(22), 7919–7928 http://dx.doi.org/10.1021/bi980355j
  • [20] MacKerell A.D., Bashford D., Bellott E.M., Dunbrack R.L., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kuchnir L., Kuczera K., Lau F.T.K., Mattos C., Michnick S., Ngo T., Nguyen D.T., Prodhom B., Reiher W.E., Roux B., Schlenkrich M., Smith J.C., Stote R., Straub J., Watanabe M., Wiórkiewicz-Kuczera J., Yin D., Karplus M., All-atom empirical potential for molecular modeling and dynamics studies of proteins, The Journal of Physical Chemistry B, 1998, 102(18), 3586–3616 http://dx.doi.org/10.1021/jp973084f
  • [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
  • [22] Rinaldo D., Field M.J., A computational study of the open and closed forms of the N-lobe human serum transferrin apoprotein, Biophys. J., 2003, 85(6), 3485–3501 http://dx.doi.org/10.1016/S0006-3495(03)74769-9
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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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