Revisiting and parallelizing SHAKE

Authors:
Yael Weinbach;Ron Elber
Affiliations:
The Hebrew University, Department of Computer Science, Givat Ram, Jerusalem 91904, Israel;Cornell University, Department of Computer Science, Ithaca, NY 14853, USA
Venue:
Journal of Computational Physics
Year:
2005

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Abstract

An algorithm is presented for running SHAKE in parallel. SHAKE is a widely used approach to compute molecular dynamics trajectories with constraints. An essential step in SHAKE is the solution of a sparse linear problem of the type Ax=b, where x is a vector of unknowns. Conjugate gradient minimization (that can be done in parallel) replaces the widely used iteration process that is inherently serial. Numerical examples present good load balancing and are limited only by communication time.