Literature DB >> 27389203

Bayesian calibration of coarse-grained forces: Efficiently addressing transferability.

Paul N Patrone1, Thomas W Rosch1, Frederick R Phelan1.   

Abstract

Generating and calibrating forces that are transferable across a range of state-points remains a challenging task in coarse-grained (CG) molecular dynamics. In this work, we present a coarse-graining workflow, inspired by ideas from uncertainty quantification and numerical analysis, to address this problem. The key idea behind our approach is to introduce a Bayesian correction algorithm that uses functional derivatives of CG simulations to rapidly and inexpensively recalibrate initial estimates f0 of forces anchored by standard methods such as force-matching. Taking density-temperature relationships as a running example, we demonstrate that this algorithm, in concert with various interpolation schemes, can be used to efficiently compute physically reasonable force curves on a fine grid of state-points. Importantly, we show that our workflow is robust to several choices available to the modeler, including the interpolation schemes and tools used to construct f0. In a related vein, we also demonstrate that our approach can speed up coarse-graining by reducing the number of atomistic simulations needed as inputs to standard methods for generating CG forces.

Entities:  

Year:  2016        PMID: 27389203      PMCID: PMC5087108          DOI: 10.1063/1.4945380

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


  18 in total

1.  Thermodynamic transferability of coarse-grained potentials for polymer-additive systems.

Authors:  Emiliano Brini; Claudia R Herbers; Gregor Deichmann; Nico F A van der Vegt
Journal:  Phys Chem Chem Phys       Date:  2012-06-22       Impact factor: 3.676

2.  Temperature dependence of coarse-grained potentials for liquid hexane.

Authors:  Karim Farah; Aoife Catherine Fogarty; Michael Christian Böhm; Florian Müller-Plathe
Journal:  Phys Chem Chem Phys       Date:  2010-12-15       Impact factor: 3.676

3.  The multiscale coarse-graining method. IX. A general method for construction of three body coarse-grained force fields.

Authors:  Avisek Das; Hans C Andersen
Journal:  J Chem Phys       Date:  2012-05-21       Impact factor: 3.488

4.  The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation.

Authors:  Avisek Das; Hans C Andersen
Journal:  J Chem Phys       Date:  2009-07-21       Impact factor: 3.488

5.  The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures.

Authors:  Vinod Krishna; Will G Noid; Gregory A Voth
Journal:  J Chem Phys       Date:  2009-07-14       Impact factor: 3.488

6.  Multiscale simulation of soft matter systems.

Authors:  Christine Peter; Kurt Kremer
Journal:  Faraday Discuss       Date:  2010       Impact factor: 4.008

7.  How short is too short for the interactions of a water potential? Exploring the parameter space of a coarse-grained water model using uncertainty quantification.

Authors:  Liam C Jacobson; Robert M Kirby; Valeria Molinero
Journal:  J Phys Chem B       Date:  2014-03-19       Impact factor: 2.991

8.  Transferable potentials for phase equilibria-coarse-grain description for linear alkanes.

Authors:  Katie A Maerzke; J Ilja Siepmann
Journal:  J Phys Chem B       Date:  2011-03-11       Impact factor: 2.991

9.  Transferability of coarse-grained force fields: the polymer case.

Authors:  Paola Carbone; Hossein Ali Karimi Varzaneh; Xiaoyu Chen; Florian Müller-Plathe
Journal:  J Chem Phys       Date:  2008-02-14       Impact factor: 3.488

10.  Coarse-grained models for fluids and their mixtures: Comparison of Monte Carlo studies of their phase behavior with perturbation theory and experiment.

Authors:  B M Mognetti; P Virnau; L Yelash; W Paul; K Binder; M Müller; L G MacDowell
Journal:  J Chem Phys       Date:  2009-01-28       Impact factor: 3.488

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  2 in total

1.  Towards a priori uncertainty quantification in coarse-grained molecular dynamics: Generalized multipole potentials.

Authors:  Paul N Patrone; Andrew M Dienstfrey; Geoffrey B McFadden
Journal:  AIAA J       Date:  2019       Impact factor: 2.127

2.  Model reduction of rigid-body molecular dynamics via generalized multipole potentials.

Authors:  Paul N Patrone; Andrew Dienstfrey; G B McFadden
Journal:  Phys Rev E       Date:  2019-12       Impact factor: 2.529

  2 in total

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