Paper Citing NAMD - Abstract
Tempkin, Jeremy O. B.; Qi, Bo; Saunders, Marissa G.; Roux, Benoit; Dinner, Aaron R.; Weare, Jonathan
Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 184114, MAY 14 2014
Iterative procedures for optimizing properties of molecular models often converge slowly owing to the computational cost of accurately representing features of interest. Here, we introduce a preconditioning scheme that allows one to use a less expensive model to guide exploration of the energy landscape of a more expensive model and thus speed the discovery of locally stable states of the latter. We illustrate our approach in the contexts of energy minimization and the string method for finding transition pathways. The relation of the method to other multilevel simulation techniques and possible extensions are discussed. (C) 2014 AIP Publishing LLC.
