Large-Scale Normal Coordinate Analysis for Molecular Structures

Authors:
Chao Yang;Barry W. Peyton;Donald W. Noid;Bobby G. Sumpter;Robert E. Tuzun
Affiliations:
-;-;-;-;-
Venue:
SIAM Journal on Scientific Computing
Year:
2001

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Abstract

We apply truncated RQ-iteration (TRQ) and the Jacobi--Davidson (JD) method to perform vibrational (eigenvalue) analysis for large-scale molecular systems. Both algorithms employ a preconditioned iterative solver to construct a low-dimensional subspace that contains desired vibrational modes. We discuss several strategies for speeding up the eigenvalue calculation. In particular, we illustrate how to construct effective preconditioners and analyze the quality of these preconditioners. We show that convergence can be improved by choosing appropriate shifts and deflating the translational and rotational modes. Numerical examples are provided to demonstrate the efficiency of our computation.