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An efficient implementation of a QM–MM method in SIESTA

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Abstract

We present the major features of a new implementation of a QM–MM method that uses the DFT code Siesta to treat the quantum mechanical subsystem and the AMBER force field to deal with the classical part. The computation of the electrostatic interaction has been completely revamped to treat periodic boundary conditions exactly, using a real-space grid that encompasses the whole system. Additionally, we present a new parallelization of the Siesta grid operations that provides near-perfect load balancing for all the relevant operations and achieves a much better scalability, which is important for efficient massive QM–MM calculations in which the grid can potentially be very large.

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Notes

  1. The large system size implies a large total memory requirement, which reflects in a slow-down for execution in a small number of processors due to swapping, cache misses, etc.

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Acknowledgments

This work was supported by the Spanish Ministry of Science and Innovation (MICINN) through grants CSD2007-00050 (Supercomputing and e-Science), and FIS2009-12721-C04. C.S.-N. acknowledges support from MICINN through the Ramon y Cajal Program.

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Authors and Affiliations

  1. Centre d’Investigacio en Nanociencia i Nanotecnologia (CIN2-CSIC/ICN), Campus UAB, Bellaterra, Spain

    Carlos F. Sanz-Navarro & Pablo Ordejón

  2. Barcelona Supercomputer Center (BSC), Barcelona, Spain

    Rogeli Grima, Edgar A. Bea, Alejandro Soba & José M. Cela

  3. Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, Bellaterra, Spain

    Alberto García

Authors
  1. Carlos F. Sanz-Navarro
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  2. Rogeli Grima
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  3. Alberto García
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  4. Edgar A. Bea
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  5. Alejandro Soba
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  6. José M. Cela
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  7. Pablo Ordejón
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Correspondence to Pablo Ordejón.

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Published as part of the special issue celebrating theoretical and computational chemistry in Spain.

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Sanz-Navarro, C.F., Grima, R., García, A. et al. An efficient implementation of a QM–MM method in SIESTA. Theor Chem Acc 128, 825–833 (2011). https://doi.org/10.1007/s00214-010-0816-5

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