Literature DB >> 21186847

Communication: Hybrid ensembles for improved force matching.

Lee-Ping Wang1, Troy Van Voorhis.   

Abstract

Force matching is a method for parameterizing empirical potentials in which the empirical parameters are fitted to a reference potential energy surface (PES). Typically, training data are sampled from a canonical ensemble generated with either the empirical potential or the reference PES. In this Communication, we show that sampling from either ensemble risks excluding critical regions of configuration space, leading to fitted potentials that deviate significantly from the reference PES. We present a hybrid ensemble which combines the Boltzmann probabilities of both potential surfaces into the fitting procedure, and we demonstrate that this technique improves the quality and stability of empirical potentials.

Year:  2010        PMID: 21186847     DOI: 10.1063/1.3519043

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


  8 in total

1.  Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches.

Authors:  Phillip S Hudson; Félix Aviat; Rubén Meana-Pañeda; Luke Warrensford; Benjamin C Pollard; Samarjeet Prasad; Michael R Jones; H Lee Woodcock; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2022-05-22       Impact factor: 4.179

2.  Systematic improvement of a classical molecular model of water.

Authors:  Lee-Ping Wang; Teresa Head-Gordon; Jay W Ponder; Pengyu Ren; John D Chodera; Peter K Eastman; Todd J Martinez; Vijay S Pande
Journal:  J Phys Chem B       Date:  2013-08-14       Impact factor: 2.991

3.  Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett's Acceptance Ratio Methods.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Theory Comput       Date:  2019-09-17       Impact factor: 6.006

4.  Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale.

Authors:  Phillip S Hudson; Kyungreem Han; H Lee Woodcock; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2018-10-01       Impact factor: 3.686

5.  A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge.

Authors:  Mahdi Ghorbani; Phillip S Hudson; Michael R Jones; Félix Aviat; Rubén Meana-Pañeda; Jeffery B Klauda; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2021-05-03       Impact factor: 3.686

6.  The Good, the Bad, and the Ugly: "HiPen", a New Dataset for Validating (S)QM/MM Free Energy Simulations.

Authors:  Fiona L Kearns; Luke Warrensford; Stefan Boresch; H Lee Woodcock
Journal:  Molecules       Date:  2019-02-14       Impact factor: 4.411

7.  Revealing solvent-dependent folding behavior of mycolic acids from Mycobacterium tuberculosis by advanced simulation analysis.

Authors:  Wilma Groenewald; Ricardo A Parra-Cruz; Christof M Jäger; Anna K Croft
Journal:  J Mol Model       Date:  2019-02-14       Impact factor: 1.810

8.  Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching.

Authors:  Phillip S Hudson; Stefan Boresch; David M Rogers; H Lee Woodcock
Journal:  J Chem Theory Comput       Date:  2018-11-15       Impact factor: 6.006

  8 in total

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