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CCMA: A Robust, Parallelizable Constraint Method for Molecular Simulations

Overview
Journal J Chem Theory Comput
Publisher American Chemical Society
Specialties Biochemistry
Chemistry
Date 2010 Jun 22
PMID 20563234
Citations 34
Authors
Peter Eastman
Vijay S Pande
Affiliations
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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.

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