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Constant Constraint Matrix Approximation: A Robust, Parallelizable Constraint Method for Molecular Simulations
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DOI：10.1021/ct900463w.png)
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Abstract
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We introduce a new algorithm, the constant constraint matrix approximation (CCMA), for constraining distances in molecular simulations. It combines the best features of many existing algorithms while avoiding their defects: it is fast and stable, can be applied to arbitrary constraint topologies, and can be efficiently implemented on modern parallel architectures. We test it on a protein with bond length and limited angle constraints and find that it requires less than one-sixth as many iterations as SHAKE to converge.
Keywords:
DYNAMICS SIMULATIONS
LAMBDA-REPRESSOR
SHAKE
ALGORITHM
EQUATIONS
MODELS
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