Literature DB >> 28049338

Fusing heterogeneous data for the calibration of molecular dynamics force fields using hierarchical Bayesian models.

Stephen Wu1, Panagiotis Angelikopoulos1, Gerardo Tauriello1, Costas Papadimitriou2, Petros Koumoutsakos1.   

Abstract

We propose a hierarchical Bayesian framework to systematically integrate heterogeneous data for the calibration of force fields in Molecular Dynamics (MD) simulations. Our approach enables the fusion of diverse experimental data sets of the physico-chemical properties of a system at different thermodynamic conditions. We demonstrate the value of this framework for the robust calibration of MD force-fields for water using experimental data of its diffusivity, radial distribution function, and density. In order to address the high computational cost associated with the hierarchical Bayesian models, we develop a novel surrogate model based on the empirical interpolation method. Further computational savings are achieved by implementing a highly parallel transitional Markov chain Monte Carlo technique. The present method bypasses possible subjective weightings of the experimental data in identifying MD force-field parameters.

Entities:  

Year:  2016        PMID: 28049338     DOI: 10.1063/1.4967956

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


  2 in total

1.  Cotranslational folding stimulates programmed ribosomal frameshifting in the alphavirus structural polyprotein.

Authors:  Haley R Harrington; Matthew H Zimmer; Laura M Chamness; Veronica Nash; Wesley D Penn; Thomas F Miller; Suchetana Mukhopadhyay; Jonathan P Schlebach
Journal:  J Biol Chem       Date:  2020-03-13       Impact factor: 5.157

2.  Data driven inference for the repulsive exponent of the Lennard-Jones potential in molecular dynamics simulations.

Authors:  Lina Kulakova; Georgios Arampatzis; Panagiotis Angelikopoulos; Panagiotis Hadjidoukas; Costas Papadimitriou; Petros Koumoutsakos
Journal:  Sci Rep       Date:  2017-11-29       Impact factor: 4.379

  2 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.