An efficient implementation of a QM-MM method in SIESTA

被引:33
|
作者
Sanz-Navarro, Carlos F. [1 ]
Grima, Rogeli [2 ]
Garcia, Alberto [3 ]
Bea, Edgar A. [2 ]
Soba, Alejandro [2 ]
Cela, Jose M. [2 ]
Ordejon, Pablo [1 ]
机构
[1] Ctr Invest Nanociencia & Nanotecnol CIN2 CSIC ICN, Bellaterra, Spain
[2] BSC, Barcelona, Spain
[3] Inst Ciencia Mat Barcelona ICMAB CSIC, Bellaterra, Spain
关键词
Density functional theory; Molecular mechanics; Parallelization; Load balancing; MOLECULAR-DYNAMICS SIMULATION; LIQUID WATER; GUANYLATE-CYCLASE; HEME-PROTEINS; QUANTUM; SYSTEMS; SOLVENTS; H2O;
D O I
10.1007/s00214-010-0816-5
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
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.
引用
收藏
页码:825 / 833
页数:9
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