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Title of article :
Parallel multilevel preconditioned conjugate-gradient approach to variable-charge molecular dynamics Original Research Article
Author/Authors :
Aiichiro Nakano، نويسنده ,
Issue Information :
دوهفته نامه با شماره پیاپی سال 1997
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Abstract :
Physical realism of molecular dynamics (MD) simulations is greatly enhanced by incorporating variable atomic charges which adapt to the local environment dynamically. In the electrostatic plus (ES+) model, atomic charges are determined to equalize electronegativity. However, this model involves costly minimization of the electrostatic energy at each MD step. A preconditioned conjugate-gradient method is developed for this minimization problem by splitting the Coulomb-interaction matrix into short- and long-range components; the computationally less intensive short-range matrix is used as a preconditioner. This preconditioning scheme is found to speed up the convergence significantly. Numerical tests involving up to 26.5 million atoms are performed on a parallel computer, and the preconditioner is shown to improve the parallel efficiency by increasing data locality. The computational cost is further amortized due to the algorithmic similarity to the multiple-time-scale MD.
Journal title :
Computer Physics Communications
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