An efficient implementation of a QM–MM method in SIESTA

Autor: Pablo Ordejón, Alberto García, José María Cela, Alejandro Soba, C F Sanz-Navarro, Rogeli Grima, Edgar Alejandro Bea
Přispěvatelé: Ministerio de Ciencia e Innovación (España), Consejo Superior de Investigaciones Científicas (España), European Commission
Rok vydání: 2010
Předmět:
Zdroj: Digital.CSIC. Repositorio Institucional del CSIC
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ISSN: 1432-2234
1432-881X
DOI: 10.1007/s00214-010-0816-5
Popis: 9 páginas, 5 figuras, 2 tablas.-- El pdf del artículo es la versión de autor.-- et al.
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.
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.
Databáze: OpenAIRE
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