Literature DB >> 28800233

Machine Learning Force Field Parameters from Ab Initio Data.

Ying Li1, Hui Li2, Frank C Pickard3, Badri Narayanan4, Fatih G Sen4, Maria K Y Chan4,5, Subramanian K R S Sankaranarayanan4,5, Bernard R Brooks3, Benoît Roux2,4,5.   

Abstract

Machine learning (ML) techniques with the genetic algorithm (GA) have been applied to determine a polarizable force field parameters using only ab initio data from quantum mechanics (QM) calculations of molecular clusters at the MP2/6-31G(d,p), DFMP2(fc)/jul-cc-pVDZ, and DFMP2(fc)/jul-cc-pVTZ levels to predict experimental condensed phase properties (i.e., density and heat of vaporization). The performance of this ML/GA approach is demonstrated on 4943 dimer electrostatic potentials and 1250 cluster interaction energies for methanol. Excellent agreement between the training data set from QM calculations and the optimized force field model was achieved. The results were further improved by introducing an offset factor during the machine learning process to compensate for the discrepancy between the QM calculated energy and the energy reproduced by optimized force field, while maintaining the local "shape" of the QM energy surface. Throughout the machine learning process, experimental observables were not involved in the objective function, but were only used for model validation. The best model, optimized from the QM data at the DFMP2(fc)/jul-cc-pVTZ level, appears to perform even better than the original AMOEBA force field (amoeba09.prm), which was optimized empirically to match liquid properties. The present effort shows the possibility of using machine learning techniques to develop descriptive polarizable force field using only QM data. The ML/GA strategy to optimize force fields parameters described here could easily be extended to other molecular systems.

Entities:  

Year:  2017        PMID: 28800233      PMCID: PMC5931379          DOI: 10.1021/acs.jctc.7b00521

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  32 in total

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Authors:  Alexander D Mackerell
Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

2.  Distributed Multipole Analysis:  Stability for Large Basis Sets.

Authors:  Anthony J Stone
Journal:  J Chem Theory Comput       Date:  2005-11       Impact factor: 6.006

3.  eReaxFF: A Pseudoclassical Treatment of Explicit Electrons within Reactive Force Field Simulations.

Authors:  Md Mahbubul Islam; Grigory Kolesov; Toon Verstraelen; Efthimios Kaxiras; Adri C T van Duin
Journal:  J Chem Theory Comput       Date:  2016-07-25       Impact factor: 6.006

4.  Global optimization of parameters in the reactive force field ReaxFF for SiOH.

Authors:  Henrik R Larsson; Adri C T van Duin; Bernd Hartke
Journal:  J Comput Chem       Date:  2013-07-15       Impact factor: 3.376

5.  Determination of best-fit potential parameters for a reactive force field using a genetic algorithm.

Authors:  Poonam Pahari; Shashank Chaturvedi
Journal:  J Mol Model       Date:  2011-06-11       Impact factor: 1.810

6.  Flexible, ab initio potential, and dipole moment surfaces for water. I. Tests and applications for clusters up to the 22-mer.

Authors:  Yimin Wang; Xinchuan Huang; Benjamin C Shepler; Bastiaan J Braams; Joel M Bowman
Journal:  J Chem Phys       Date:  2011-03-07       Impact factor: 3.488

7.  Transferable next-generation force fields from simple liquids to complex materials.

Authors:  J R Schmidt; Kuang Yu; Jesse G McDaniel
Journal:  Acc Chem Res       Date:  2015-02-17       Impact factor: 22.384

8.  Next-Generation Force Fields from Symmetry-Adapted Perturbation Theory.

Authors:  Jesse G McDaniel; J R Schmidt
Journal:  Annu Rev Phys Chem       Date:  2016-03-16       Impact factor: 12.703

9.  Ab Initio-Based Bond Order Potential to Investigate Low Thermal Conductivity of Stanene Nanostructures.

Authors:  Mathew J Cherukara; Badri Narayanan; Alper Kinaci; Kiran Sasikumar; Stephen K Gray; Maria K Y Chan; Subramanian K R S Sankaranarayanan
Journal:  J Phys Chem Lett       Date:  2016-09-12       Impact factor: 6.475

10.  Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field.

Authors:  Hui Li; Van Ngo; Mauricio Chagas Da Silva; Dennis R Salahub; Karen Callahan; Benoît Roux; Sergei Yu Noskov
Journal:  J Phys Chem B       Date:  2015-02-04       Impact factor: 2.991

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  10 in total

1.  Better force fields start with better data: A data set of cation dipeptide interactions.

Authors:  Xiaojuan Hu; Maja-Olivia Lenz-Himmer; Carsten Baldauf
Journal:  Sci Data       Date:  2022-06-17       Impact factor: 8.501

2.  Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models.

Authors:  Owen C Madin; Simon Boothroyd; Richard A Messerly; Josh Fass; John D Chodera; Michael R Shirts
Journal:  J Chem Inf Model       Date:  2022-02-07       Impact factor: 6.162

3.  Accelerating prediction of chemical shift of protein structures on GPUs: Using OpenACC.

Authors:  Eric Wright; Mauricio H Ferrato; Alexander J Bryer; Robert Searles; Juan R Perilla; Sunita Chandrasekaran
Journal:  PLoS Comput Biol       Date:  2020-05-13       Impact factor: 4.475

4.  Improvement of the Force Field for β-d-Glucose with Machine Learning.

Authors:  Makoto Ikejo; Hirofumi Watanabe; Kohei Shimamura; Shigenori Tanaka
Journal:  Molecules       Date:  2021-11-05       Impact factor: 4.411

5.  MolE8: finding DFT potential energy surface minima values from force-field optimised organic molecules with new machine learning representations.

Authors:  Sanha Lee; Kristaps Ermanis; Jonathan M Goodman
Journal:  Chem Sci       Date:  2022-05-28       Impact factor: 9.969

6.  The TensorMol-0.1 model chemistry: a neural network augmented with long-range physics.

Authors:  Kun Yao; John E Herr; David W Toth; Ryker Mckintyre; John Parkhill
Journal:  Chem Sci       Date:  2018-01-18       Impact factor: 9.825

Review 7.  On flexible force fields for metal-organic frameworks: Recent developments and future prospects.

Authors:  Jurn Heinen; David Dubbeldam
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2018-03-25

8.  The automated optimisation of a coarse-grained force field using free energy data.

Authors:  Javier Caceres-Delpiano; Lee-Ping Wang; Jonathan W Essex
Journal:  Phys Chem Chem Phys       Date:  2021-11-10       Impact factor: 3.676

9.  Automated fitting of transition state force fields for biomolecular simulations.

Authors:  Taylor R Quinn; Himani N Patel; Kevin H Koh; Brandon E Haines; Per-Ola Norrby; Paul Helquist; Olaf Wiest
Journal:  PLoS One       Date:  2022-03-10       Impact factor: 3.240

Review 10.  Biophysical analysis of SARS-CoV-2 transmission and theranostic development via N protein computational characterization.

Authors:  Godfred O Sabbih; Maame A Korsah; Jaison Jeevanandam; Michael K Danquah
Journal:  Biotechnol Prog       Date:  2020-11-09
  10 in total

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