Literature DB >> 24328448

Advanced potential energy surfaces for condensed phase simulation.

Omar Demerdash1, Eng-Hui Yap, Teresa Head-Gordon.   

Abstract

Computational modeling at the atomistic and mesoscopic levels has undergone dramatic development in the past 10 years to meet the challenge of adequately accounting for the many-body nature of intermolecular interactions. At the heart of this challenge is the ability to identify the strengths and specific limitations of pairwise-additive interactions, to improve classical models to explicitly account for many-body effects, and consequently to enhance their ability to describe a wider range of reference data and build confidence in their predictive capacity. However, the corresponding computational cost of these advanced classical models increases significantly enough that statistical convergence of condensed phase observables becomes more difficult to achieve. Here we review a hierarchy of potential energy surface models used in molecular simulations for systems with many degrees of freedom that best meet the trade-off between accuracy and computational speed in order to define a sweet spot for a given scientific problem of interest.

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Year:  2013        PMID: 24328448     DOI: 10.1146/annurev-physchem-040412-110040

Source DB:  PubMed          Journal:  Annu Rev Phys Chem        ISSN: 0066-426X            Impact factor:   12.703


  10 in total

1.  Efficient treatment of induced dipoles.

Authors:  Andrew C Simmonett; Frank C Pickard; Yihan Shao; Thomas E Cheatham; Bernard R Brooks
Journal:  J Chem Phys       Date:  2015-08-21       Impact factor: 3.488

2.  An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Authors:  Jing Huang; Ye Mei; Gerhard König; Andrew C Simmonett; Frank C Pickard; Qin Wu; Lee-Ping Wang; Alexander D MacKerell; Bernard R Brooks; Yihan Shao
Journal:  J Chem Theory Comput       Date:  2017-01-24       Impact factor: 6.006

Review 3.  Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

Authors:  A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

Review 4.  Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?

Authors:  Pnina Dauber-Osguthorpe; A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

5.  Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions.

Authors:  Ye Mei; Andrew C Simmonett; Frank C Pickard; Robert A DiStasio; Bernard R Brooks; Yihan Shao
Journal:  J Phys Chem A       Date:  2015-05-18       Impact factor: 2.781

6.  PB-AM: An open-source, fully analytical linear poisson-boltzmann solver.

Authors:  Lisa E Felberg; David H Brookes; Eng-Hui Yap; Elizabeth Jurrus; Nathan A Baker; Teresa Head-Gordon
Journal:  J Comput Chem       Date:  2016-11-02       Impact factor: 3.376

7.  Finding Our Way in the Dark Proteome.

Authors:  Asmit Bhowmick; David H Brookes; Shane R Yost; H Jane Dyson; Julie D Forman-Kay; Daniel Gunter; Martin Head-Gordon; Gregory L Hura; Vijay S Pande; David E Wemmer; Peter E Wright; Teresa Head-Gordon
Journal:  J Am Chem Soc       Date:  2016-07-19       Impact factor: 15.419

Review 8.  Advanced Potential Energy Surfaces for Molecular Simulation.

Authors:  Alex Albaugh; Henry A Boateng; Richard T Bradshaw; Omar N Demerdash; Jacek Dziedzic; Yuezhi Mao; Daniel T Margul; Jason Swails; Qiao Zeng; David A Case; Peter Eastman; Lee-Ping Wang; Jonathan W Essex; Martin Head-Gordon; Vijay S Pande; Jay W Ponder; Yihan Shao; Chris-Kriton Skylaris; Ilian T Todorov; Mark E Tuckerman; Teresa Head-Gordon
Journal:  J Phys Chem B       Date:  2016-09-22       Impact factor: 3.466

9.  Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations.

Authors:  Kevin Hauser; Christopher Negron; Steven K Albanese; Soumya Ray; Thomas Steinbrecher; Robert Abel; John D Chodera; Lingle Wang
Journal:  Commun Biol       Date:  2018-06-13

10.  Ab initio molecular dynamics simulations of liquid water using high quality meta-GGA functionals.

Authors:  Luis Ruiz Pestana; Narbe Mardirossian; Martin Head-Gordon; Teresa Head-Gordon
Journal:  Chem Sci       Date:  2017-02-27       Impact factor: 9.825

  10 in total

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