Literature DB >> 15268541

Determination of solvation free energies by adaptive expanded ensemble molecular dynamics.

K Magnus Aberg1, Alexander P Lyubartsev, Sven P Jacobsson, Aatto Laaksonen.   

Abstract

A new method of calculating absolute free energies is presented. It was developed as an extension to the expanded ensemble molecular dynamics scheme and uses probability density estimation to continuously optimize the expanded ensemble parameters. The new method is much faster as it removes the time-consuming and expertise-requiring step of determining balancing factors. Its efficiency and accuracy are demonstrated for the dissolution of three qualitatively very different chemical species in water: methane, ionic salts, and benzylamine. A recently suggested optimization scheme by Wang and Landau [Phys. Rev. Lett. 86, 2050 (2001)] was also implemented and found to be computationally less efficient than the proposed adaptive expanded ensemble method. (c) 2004 American Institute of Physics.

Entities:  

Year:  2004        PMID: 15268541     DOI: 10.1063/1.1642601

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


  1 in total

1.  Binding energy calculations for hevein-carbohydrate interactions using expanded ensemble molecular dynamics simulations.

Authors:  Chaitanya A K Koppisetty; Martin Frank; Alexander P Lyubartsev; Per-Georg Nyholm
Journal:  J Comput Aided Mol Des       Date:  2014-11-29       Impact factor: 3.686

  1 in total

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