Literature DB >> 24832260

Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations.

Jeremy O B Tempkin1, Bo Qi1, Marissa G Saunders1, Benoit Roux1, Aaron R Dinner1, Jonathan Weare2.   

Abstract

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.

Mesh:

Year:  2014        PMID: 24832260     DOI: 10.1063/1.4872021

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  4 in total

1.  Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics - Monte Carlo Canonical Propagation Algorithm.

Authors:  Yunjie Chen; Seyit Kale; Jonathan Weare; Aaron R Dinner; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2016-03-25       Impact factor: 6.006

Review 2.  Whole-Cell Models and Simulations in Molecular Detail.

Authors:  Michael Feig; Yuji Sugita
Journal:  Annu Rev Cell Dev Biol       Date:  2019-07-12       Impact factor: 13.827

3.  Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.

Authors:  Parimal Kar; Michael Feig
Journal:  J Chem Theory Comput       Date:  2017-10-19       Impact factor: 6.006

4.  Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol.

Authors:  Seyit Kale; Olaseni Sode; Jonathan Weare; Aaron R Dinner
Journal:  J Chem Theory Comput       Date:  2014-11-07       Impact factor: 6.006

  4 in total

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