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Acceleration of Ab Initio QM/MM Calculations under Periodic Boundary Conditions by Multiscale and Multiple Time Step Approaches
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
2014 (Engelska)Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, nr 10, s. 4175-4183Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Development of multiscale ab initio quantum mechanical and molecular mechanical (AI-QM/MM) method for periodic boundary molecular dynamics (MD) simulations and their acceleration by multiple time step approach are described. The developed method achieves accuracy and efficiency by integrating the AI-QM/MM level of theory and the previously developed semiempirical (SE) QM/MM-Ewald sum method [J. Chem. Theory Comput. 2005, 1, 2] extended to the smooth particle-mesh Ewald (PME) summation method. In the developed methods, the total energy of the simulated system is evaluated at the SE-QM/MM-PME level of theory to include long-range QM/MM electrostatic interactions, which is then corrected on the fly using the AI-QM/MM level of theory within the real space cutoff. The resulting energy expression enables decomposition of total forces applied to each atom into forces determined at the low-level SE-QM/MM method and correction forces at the AI-QM/MM level, to integrate the system using the reversible reference system propagator algorithm. The resulting method achieves a substantial speed-up of the entire calculation by minimizing the number of time-consuming energy and gradient evaluations at the AI-QM/MM level. Test calculations show that the developed multiple time step AI-QM/MM method yields MD trajectories and potential of mean force profiles comparable to single time step QM/MM results. The developed method, together with message passing interface (MPI) parallelization, accelerates the present AI-QM/MM MD simulations about 30-fold relative to the speed of single-core AI-QM/MM simulations for the molecular systems tested in the present work, making the method less than one order slower than the SE-QM/MM methods under periodic boundary conditions.

Ort, förlag, år, upplaga, sidor
2014. Vol. 10, nr 10, s. 4175-4183
Nyckelord [en]
LEEUW SW, 1980, PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES A-MATHEMATICAL, WAR MJS, 1985, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, V107, P3902
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Kemi
Identifikatorer
URN: urn:nbn:se:umu:diva-96620DOI: 10.1021/ct5005643ISI: 000343196300001OAI: oai:DiVA.org:umu-96620DiVA, id: diva2:766594
Tillgänglig från: 2014-11-27 Skapad: 2014-11-24 Senast uppdaterad: 2018-06-07Bibliografiskt granskad

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