title: CCMA: A Robust, Parallelizable Constraint Method for Molecular Simulations.
abstract: 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, 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.
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA 94305.
authors.forename: Peter
authors.initials: P
authors.lastname: Eastman
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Pande