skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Advanced Potential Energy Surfaces for Molecular Simulation

Journal Article · · Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry
 [1];  [2];  [3];  [4];  [5];  [4];  [6];  [7];  [8];  [7];  [9];  [9];  [3];  [4];  [9];  [10];  [11];  [3];  [12];  [13] more »;  [14] « less
  1. Univ. of California, Berkeley, CA (United States). Dept. of Chemical and Biomolecular Engineering
  2. Bates College, Lewiston, ME (United States). Dept. of Mathematics
  3. Univ. of Southampton (United Kingdom). School of Chemistry
  4. Univ. of California, Berkeley, CA (United States). Dept. of Chemistry
  5. Univ. of Southampton (United Kingdom). School of Chemistry; Gdansk Univ. of Technology, Gdansk (Poland). Faculty of Applied Physics and Mathematics
  6. New York Univ. (NYU), NY (United States). Dept. of Chemistry
  7. Rutgers Univ., Piscataway, NJ (United States). Dept. of Chemistry and Chemical Biology
  8. National Inst. of Health (NIH), Bethesda, MD (United States). Lab. of Computational Biology, National Heart, Lung and Blood Inst.
  9. Stanford Univ., CA (United States). Dept. of Chemistry
  10. Washington Univ., St. Louis, MO (United States). Dept. Chemistry
  11. Q-Chem Inc., Pleasanton, CA (United States)
  12. Science and Technology Facilities Council (STFC), Daresbury (United Kingdom). Daresbury Lab.
  13. New York Univ. (NYU), NY (United States). Courant Inst. of Mathematical Science, and Dept. of Chemistry; NYU-ECNU, Center for Computational Chemistry at NYU, Shanghai (China)
  14. Univ. of California, Berkeley, CA (United States). Dept. of Chemistry, Dept. of Chemical and Biomolecular Engineering, and Dept. of Bioengineering
+ Show Author Affiliations

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). Here 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. Finally, 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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22), Scientific User Facilities Division (SC-22.3 )
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1478341
Journal Information:
Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry, Vol. 120, Issue 37; ISSN 1520-6106
Publisher:
American Chemical SocietyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 63 works
Citation information provided by
Web of Science

References (160)

Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n ‐Alkane Molecules journal December 1968
The Amber biomolecular simulation programs journal January 2005
CHARMM: The biomolecular simulation program journal July 2009
Scalable molecular dynamics with NAMD journal January 2005
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation journal November 2012
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems journal June 1993
Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations journal January 2004
Simulating Hamiltonian Dynamics journal January 2009
Nosé–Hoover chains: The canonical ensemble via continuous dynamics journal August 1992
Explicit reversible integrators for extended systems dynamics journal April 1996
The Role of Broken Symmetry in Solvation of a Spherical Cavity in Classical and Quantum Water Models journal July 2014
Ions at Aqueous Interfaces: From Water Surface to Hydrated Proteins journal May 2008
Ions at Hydrophobic Aqueous Interfaces: Molecular Dynamics with Effective Polarization journal July 2012
Calculations of the Electric Fields in Liquid Solutions journal November 2013
Excited States of the Bacteriochlorophyll b Dimer of Rhodopseudomonas viridis: A QM/MM Study of the Photosynthetic Reaction Center That Includes MM Polarization journal April 1995
Optimizing Solute–Water van der Waals Interactions To Reproduce Solvation Free Energies journal April 2012
Optimizing Protein−Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides journal March 2011
Hydration Water Dynamics Near Biological Interfaces journal December 2008
Effects of co-solvents on peptide hydration water structure and dynamics journal January 2010
Advanced Potential Energy Surfaces for Condensed Phase Simulation journal April 2014
Incorporating electric polarizabilities in water-water interaction potentials journal January 1990
An effective fragment method for modeling solvent effects in quantum mechanical calculations journal August 1996
Toward a Molecular Orbital Derived Empirical Potential for Liquid Simulations journal January 1997
Fluctuating Charge, Polarizable Dipole, and Combined Models:  Parameterization from ab Initio Quantum Chemistry journal June 1999
Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases journal July 2001
Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests journal October 2002
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations journal October 2002
A simple polarizable model of water based on classical Drude oscillators journal September 2003
Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF journal December 2003
Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from ab Initio Quantum Chemistry journal January 2004
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations journal January 2003
A quantum mechanical polarizable force field for biomolecular interactions journal May 2005
Efficient Simulation Method for Polarizable Protein Force Fields:  Application to the Simulation of BPTI in Liquid Water journal December 2004
Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides journal January 2006
The bend angle of water in ice Ih and liquid water: The significance of implementing the nonlinear monomer dipole moment surface in classical interaction potentials journal May 2006
Virial Coefficients of Polarizable Water:  Applications to Thermodynamic Properties and Molecular Clustering † journal November 2007
Force field modeling of conformational energies: Importance of multipole moments and intramolecular polarization journal January 2007
Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand−Macromolecule Complexes. A Bottom-Up Strategy journal October 2007
Calculation of the Free Energy of Polarization:  Quantifying the Effect of Explicitly Treating Electronic Polarization on the Transferability of Force-Field Parameters journal June 2007
Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion journal October 2007
Polarizabilities of individual molecules and ions in liquids from first principles journal November 2008
Polarization effects in molecular mechanical force fields journal July 2009
Exploring Ion Permeation Energetics in Gramicidin A Using Polarizable Charge Equilibration Force Fields journal September 2009
Accurate Intermolecular Potentials with Physically Grounded Electrostatics journal May 2011
Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data journal November 2012
Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator journal November 2013
i-TTM Model for Ab Initio-Based Ion–Water Interaction Potentials. 1. Halide–Water Potential Energy Functions journal November 2015
Calcium Binding to Calmodulin by Molecular Dynamics with Effective Polarization journal November 2014
Accounting for Electronic Polarization Effects in Aqueous Sodium Chloride via Molecular Dynamics Aided by Neutron Scattering journal July 2015
Evaluation of charge penetration between distributed multipolar expansions journal May 2000
Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles journal January 2016
General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field journal May 2015
The effects of charge transfer on the properties of liquid water journal May 2011
Charge Transfer Models of Zinc and Magnesium in Water journal March 2015
Hydrated proton and hydroxide charge transfer at the liquid/vapor interface of water journal July 2015
Ion association in aqueous solution journal January 2016
The effects of charge transfer on the aqueous solvation of ions journal July 2012
Charge transfer effects of ions at the liquid water/vapor interface journal May 2014
Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation journal May 2003
Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules journal August 2011
Current Status of the AMOEBA Polarizable Force Field journal March 2010
Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals journal March 2011
Reversible multiple time scale molecular dynamics journal August 1992
Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning journal March 2015
Systematic Improvement of a Classical Molecular Model of Water journal August 2013
Convergence of the Many-Body Expansion for Energy and Forces for Classical Polarizable Models in the Condensed Phase journal July 2016
Introducing ONETEP : Linear-scaling density functional simulations on parallel computers journal February 2005
Advances in molecular quantum chemistry contained in the Q-Chem 4 program package journal September 2014
An efficient and stable hybrid extended Lagrangian/self-consistent field scheme for solving classical mutual induction journal November 2015
A Stochastic, Resonance-Free Multiple Time-Step Algorithm for Polarizable Models That Permits Very Large Time Steps journal April 2016
Arbitrary order permanent Cartesian multipolar electrostatic interactions journal January 2015
Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation journal July 2016
Water Molecule Interactions journal December 1970
Electrostatically embedded many-body method for dipole moments, partial atomic charges, and charge transfer journal January 2012
A generalized many-body expansion and a unified view of fragment-based methods in electronic structure theory journal August 2012
Fragmentation Methods: A Route to Accurate Calculations on Large Systems journal August 2011
Building Force Fields: An Automatic, Systematic, and Reproducible Approach journal May 2014
Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model journal September 2014
Nonorthogonal generalized Wannier function pseudopotential plane-wave method journal July 2002
Biomolecular electrostatics and solvation: a computational perspective journal November 2012
Distributed Multipole Analysis:  Stability for Large Basis Sets journal September 2005
Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in O NETEP journal June 2015
Electrostatic considerations affecting the calculated HOMO–LUMO gap in protein molecules journal March 2013
LIBEFP: A new parallel implementation of the effective fragment potential method as a portable software library journal July 2013
Effective fragment potential method in Q-CHEM : A guide for users and developers : Software News and Updates journal January 2013
A smooth particle mesh Ewald method journal November 1995
An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald journal May 2014
Psi4: an open-source ab initio electronic structure program : Psi4: an electronic structure program
  • Turney, Justin M.; Simmonett, Andrew C.; Parrish, Robert M.
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 4 https://doi.org/10.1002/wcms.93
journal October 2011
NWChem: scalable parallel computational chemistry: NWChem
  • van Dam, H. J. J.; de Jong, W. A.; Bylaska, E.
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 1, Issue 6 https://doi.org/10.1002/wcms.62
journal May 2011
Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method journal December 2002
Fast evaluation of polarizable forces journal October 2005
Convergence acceleration of iterative sequences. the case of scf iteration journal July 1980
Molecular dynamics simulation of polarizable water by an extended Lagrangian method journal October 1992
Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm journal August 2003
Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications journal August 2009
Efficient treatment of induced dipoles journal August 2015
Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations journal March 2014
Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II. Toward Massively Parallel Computations Using Smooth Particle Mesh Ewald journal May 2015
Extended Born-Oppenheimer Molecular Dynamics journal March 2008
Generalized extended Lagrangian Born-Oppenheimer molecular dynamics journal October 2014
Extended Lagrangian Born–Oppenheimer molecular dynamics with dissipation journal June 2009
Time-reversible ab initio molecular dynamics journal April 2007
A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters journal January 1982
Molecular dynamics with coupling to an external bath journal October 1984
Integrating the Car–Parrinello equations. I. Basic integration techniques journal July 1994
Long Time Molecular Dynamics for Enhanced Conformational Sampling in Biomolecular Systems journal October 2004
Stochastic, resonance-free multiple time-step algorithm for molecular dynamics with very large time steps journal December 2013
DL_MULTI—A molecular dynamics program to use distributed multipole electrostatic models to simulate the dynamics of organic crystals journal June 2008
DL_POLY_3: new dimensions in molecular dynamics simulations via massive parallelism journal January 2006
Ewald summation and reaction field methods for potentials with atomic charges, dipoles, and polarizabilities journal April 2000
Direct Wolf summation of a polarizable force field for silica journal May 2010
A DAFT DL_POLY distributed memory adaptation of the Smoothed Particle Mesh Ewald method journal September 2006
Generalized Gradient Approximation Made Simple journal October 1996
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu journal April 2010
ωB97X-V: A 10-parameter, range-separated hybrid, generalized gradient approximation density functional with nonlocal correlation, designed by a survival-of-the-fittest strategy journal January 2014
Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V journal February 2015
Property-optimized Gaussian basis sets for molecular response calculations journal October 2010
Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit journal April 2007
Structure of liquid water at ambient temperature from ab initio molecular dynamics performed in the complete basis set limit journal October 2006
Ab initio molecular dynamics study of water at constant pressure using converged basis sets and empirical dispersion corrections journal July 2012
On the connection between proton transport, structural diffusion, and reorientation of the hydrated hydroxide ion as a function of temperature journal August 2011
Ab Initio Molecular Dynamics Study of the Aqueous HOO – Ion journal April 2014
Concerted Hydrogen-Bond Dynamics in the Transport Mechanism of the Hydrated Proton: A First-Principles Molecular Dynamics Study journal November 2009
Ab Initio Molecular Dynamics with Discrete Variable Representation Basis Sets:  Techniques and Application to Liquid Water † journal April 2006
Auxiliary basis sets to approximate Coulomb potentials journal June 1995
An implementation of RI-SCF on parallel computers journal January 1997
Fast, accurate evaluation of exact exchange: The occ-RI-K algorithm journal July 2015
Efficient Implementation of the Pair Atomic Resolution of the Identity Approximation for Exact Exchange for Hybrid and Range-Separated Density Functionals journal January 2015
Dual-basis second-order Møller-Plesset perturbation theory: A reduced-cost reference for correlation calculations journal August 2006
Non-Covalent Interactions with Dual-Basis Methods: Pairings for Augmented Basis Sets journal April 2009
The SAMPL4 host–guest blind prediction challenge: an overview journal March 2014
Standard Free Energy of Releasing a Localized Water Molecule from the Binding Pockets of Proteins:  Double-Decoupling Method journal June 2004
Efficient estimation of free energy differences from Monte Carlo data journal October 1976
Calculating binding free energies of host–guest systems using the AMOEBA polarizable force field journal January 2016
Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field journal July 2016
Why do molecules interact? The origin of electron donor-acceptor complexes, hydrogen bonding and proton affinity journal August 1977
Energy decomposition analysis: Energy decomposition analysis
  • Hopffgarten, Moritz von; Frenking, Gernot
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 1 https://doi.org/10.1002/wcms.71
journal June 2011
Energy decomposition analysis approaches and their evaluation on prototypical protein–drug interaction patterns journal January 2015
Perturbation Theory Approach to Intermolecular Potential Energy Surfaces of van der Waals Complexes journal November 1994
Wavefunction methods for noncovalent interactions: Noncovalent interactions
  • Hohenstein, Edward G.; Sherrill, C. David
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 2 https://doi.org/10.1002/wcms.84
journal July 2011
Symmetry-adapted perturbation theory of intermolecular forces: Symmetry-adapted perturbation theory journal August 2011
A new energy decomposition scheme for molecular interactions within the Hartree-Fock approximation journal March 1976
Energy decomposition analysis of intermolecular interactions using a block-localized wave function approach journal April 2000
Block-Localized Wavefunction (BLW) Method at the Density Functional Theory (DFT) Level journal August 2007
Energy decomposition analysis based on a block-localized wavefunction and multistate density functional theory journal January 2011
Unravelling the Origin of Intermolecular Interactions Using Absolutely Localized Molecular Orbitals journal September 2007
Analysis of charge transfer effects in molecular complexes based on absolutely localized molecular orbitals journal May 2008
Unrestricted absolutely localized molecular orbitals for energy decomposition analysis: Theory and applications to intermolecular interactions involving radicals journal April 2013
Polarization contributions to intermolecular interactions revisited with fragment electric-field response functions journal September 2015
Alternative definitions of the frozen energy in energy decomposition analysis of density functional theory calculations journal February 2016
Defining the contributions of permanent electrostatics, Pauli repulsion, and dispersion in density functional theory calculations of intermolecular interaction energies journal March 2016
Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism journal June 2014
Insights into the catalytic mechanism of peptidyl prolyl cis/trans isomerases journal January 2004
Describing Noncovalent Interactions beyond the Common Approximations: How Accurate Is the “Gold Standard,” CCSD(T) at the Complete Basis Set Limit? journal April 2013
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs journal January 2006
Basis set convergence of the coupled-cluster correction, δMP2CCSD(T): Best practices for benchmarking non-covalent interactions and the attendant revision of the S22, NBC10, HBC6, and HSG databases journal November 2011
Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods journal December 2011
An improved treatment of empirical dispersion and a many-body energy decomposition scheme for the explicit polarization plus symmetry-adapted perturbation theory (XSAPT) method journal July 2013
Accurate and Efficient Quantum Chemistry Calculations for Noncovalent Interactions in Many-Body Systems: The XSAPT Family of Methods journal December 2014
Probing non-covalent interactions with a second generation energy decomposition analysis using absolutely localized molecular orbitals journal January 2016

Cited By (18)

Investigating coordination flexibility of glycerophosphodiesterase (GpdQ) through interactions with mono-, di-, and triphosphoester (NPP, BNPP, GPE, and paraoxon) substrates journal January 2019
Classical molecular dynamics on graphics processing unit architectures journal August 2019
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics journal July 2017
A FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics journal November 2019
Mapping the Drude polarizable force field onto a multipole and induced dipole model journal October 2017
Perturbation potentials to overcome order/disorder transitions in alchemical binding free energy calculations journal September 2019
Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science journal November 2018
Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics journal November 2018
The strengths and limitations of effective centroid force models explored by studying isotopic effects in liquid water journal May 2018
Molecular dynamics based enhanced sampling of collective variables with very large time steps journal January 2018
Inertial extended-Lagrangian scheme for solving charge equilibration models journal January 2019
Natural selection based on coordination chemistry: computational assessment of [4Fe–4S]-maquettes with non-coded amino acids journal October 2019
Secondary structure analysis of peptides with relevance to iron–sulfur cluster nesting journal December 2018
Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity
  • Huggins, David J.; Biggin, Philip C.; Dämgen, Marc A.
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 9, Issue 3 https://doi.org/10.1002/wcms.1393
journal September 2018
A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes journal October 2018
Biomolecular simulations: from dynamics and mechanisms to computational assays of biological activity text January 2019
Inertial Extended-Lagrangian Scheme for Solving Charge Equilibration Models text January 2019
Convergence of stochastic-extended Lagrangian molecular dynamics method for polarizable force field simulation journal August 2021

Similar Records

Data Locality Enhancement of Dynamic Simulations for Exascale Computing (Final Report)
Technical Report · Fri Nov 29 00:00:00 EST 2019 · OSTI ID:1478341
ECP ST Project 2.3.1.06-STPM08-RAJA (Final Report)
Technical Report · Fri Jan 24 00:00:00 EST 2020 · OSTI ID:1478341
Development of $\mathrm{AMOEBA}$ Polarizable Force Field for Rare-Earth La3+ Interaction with Bioinspired Ligands
Journal Article · Fri Feb 03 00:00:00 EST 2023 · Journal of Physical Chemistry. B · OSTI ID:1478341
+3 more

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
97 MATHEMATICS AND COMPUTING