Literature DB >> 27513316

Advanced Potential Energy Surfaces for Molecular Simulation.

Alex Albaugh, Henry A Boateng1, Richard T Bradshaw2, Omar N Demerdash, Jacek Dziedzic2,3, Yuezhi Mao, Daniel T Margul, Jason Swails4, Qiao Zeng5, David A Case4, Peter Eastman6, Lee-Ping Wang6, Jonathan W Essex2, Martin Head-Gordon, Vijay S Pande6, Jay W Ponder7, Yihan Shao8, Chris-Kriton Skylaris2, Ilian T Todorov9, Mark E Tuckerman10, Teresa Head-Gordon.   

Abstract

Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.

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Year:  2016        PMID: 27513316      PMCID: PMC9113031          DOI: 10.1021/acs.jpcb.6b06414

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   3.466


  110 in total

1.  The Amber biomolecular simulation programs.

Authors:  David A Case; Thomas E Cheatham; Tom Darden; Holger Gohlke; Ray Luo; Kenneth M Merz; Alexey Onufriev; Carlos Simmerling; Bing Wang; Robert J Woods
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

2.  Dual-basis second-order Moller-Plesset perturbation theory: A reduced-cost reference for correlation calculations.

Authors:  Ryan P Steele; Robert A DiStasio; Yihan Shao; Jing Kong; Martin Head-Gordon
Journal:  J Chem Phys       Date:  2006-08-21       Impact factor: 3.488

Review 3.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

4.  Charge transfer effects of ions at the liquid water/vapor interface.

Authors:  Marielle Soniat; Steven W Rick
Journal:  J Chem Phys       Date:  2014-05-14       Impact factor: 3.488

5.  Basis set convergence of the coupled-cluster correction, δ(MP2)(CCSD(T)): best practices for benchmarking non-covalent interactions and the attendant revision of the S22, NBC10, HBC6, and HSG databases.

Authors:  Michael S Marshall; Lori A Burns; C David Sherrill
Journal:  J Chem Phys       Date:  2011-11-21       Impact factor: 3.488

Review 6.  The SAMPL4 host-guest blind prediction challenge: an overview.

Authors:  Hari S Muddana; Andrew T Fenley; David L Mobley; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2014-03-06       Impact factor: 3.686

7.  Non-Covalent Interactions with Dual-Basis Methods: Pairings for Augmented Basis Sets.

Authors:  Ryan P Steele; Robert A DiStasio; Martin Head-Gordon
Journal:  J Chem Theory Comput       Date:  2009-04-30       Impact factor: 6.006

8.  Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles.

Authors:  Christophe Narth; Louis Lagardère; Étienne Polack; Nohad Gresh; Qiantao Wang; David R Bell; Joshua A Rackers; Jay W Ponder; Pengyu Y Ren; Jean-Philip Piquemal
Journal:  J Comput Chem       Date:  2016-02-15       Impact factor: 3.376

9.  An efficient and stable hybrid extended Lagrangian/self-consistent field scheme for solving classical mutual induction.

Authors:  Alex Albaugh; Omar Demerdash; Teresa Head-Gordon
Journal:  J Chem Phys       Date:  2015-11-07       Impact factor: 3.488

10.  Calculation of the free energy of polarization: quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters.

Authors:  Daan P Geerke; Wilfred F van Gunsteren
Journal:  J Phys Chem B       Date:  2007-05-18       Impact factor: 2.991

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  16 in total

1.  Toward Learned Chemical Perception of Force Field Typing Rules.

Authors:  Camila Zanette; Caitlin C Bannan; Christopher I Bayly; Josh Fass; Michael K Gilson; Michael R Shirts; John D Chodera; David L Mobley
Journal:  J Chem Theory Comput       Date:  2018-12-24       Impact factor: 6.006

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

4.  Perspective: Quantum mechanical methods in biochemistry and biophysics.

Authors:  Qiang Cui
Journal:  J Chem Phys       Date:  2016-10-14       Impact factor: 3.488

5.  On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces.

Authors:  Gerhard König; Sereina Riniker
Journal:  Interface Focus       Date:  2020-10-16       Impact factor: 3.906

6.  Mapping the Drude polarizable force field onto a multipole and induced dipole model.

Authors:  Jing Huang; Andrew C Simmonett; Frank C Pickard; Alexander D MacKerell; Bernard R Brooks
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

7.  Natural selection based on coordination chemistry: computational assessment of [4Fe-4S]-maquettes with non-coded amino acids.

Authors:  Robert K Szilagyi; Rebecca Hanscam; Eric M Shepard; Shawn E McGlynn
Journal:  Interface Focus       Date:  2019-10-18       Impact factor: 3.906

8.  Non-covalent interactions from a Quantum Chemical Topology perspective.

Authors:  Paul L A Popelier
Journal:  J Mol Model       Date:  2022-08-25       Impact factor: 2.172

9.  The strengths and limitations of effective centroid force models explored by studying isotopic effects in liquid water.

Authors:  Ying Yuan; Jicun Li; Xin-Zheng Li; Feng Wang
Journal:  J Chem Phys       Date:  2018-05-14       Impact factor: 3.488

10.  OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

Authors:  Peter Eastman; Jason Swails; John D Chodera; Robert T McGibbon; Yutong Zhao; Kyle A Beauchamp; Lee-Ping Wang; Andrew C Simmonett; Matthew P Harrigan; Chaya D Stern; Rafal P Wiewiora; Bernard R Brooks; Vijay S Pande
Journal:  PLoS Comput Biol       Date:  2017-07-26       Impact factor: 4.475

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