Constant Constraint Matrix Approximation: A Robust, Parallelizable Constraint Method for Molecular Simulations

摘要

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.