Advanced Potential Energy Surfaces for Molecular Simulation
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). 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 functionalmore »
- Authors:
-
more »
- Univ. of California, Berkeley, CA (United States). Dept. of Chemical and Biomolecular Engineering
- Bates College, Lewiston, ME (United States). Dept. of Mathematics
- Univ. of Southampton (United Kingdom). School of Chemistry
- Univ. of California, Berkeley, CA (United States). Dept. of Chemistry
- Univ. of Southampton (United Kingdom). School of Chemistry; Gdansk Univ. of Technology, Gdansk (Poland). Faculty of Applied Physics and Mathematics
- New York Univ. (NYU), NY (United States). Dept. of Chemistry
- Rutgers Univ., Piscataway, NJ (United States). Dept. of Chemistry and Chemical Biology
- National Inst. of Health (NIH), Bethesda, MD (United States). Lab. of Computational Biology, National Heart, Lung and Blood Inst.
- Stanford Univ., CA (United States). Dept. of Chemistry
- Washington Univ., St. Louis, MO (United States). Dept. Chemistry
- Q-Chem Inc., Pleasanton, CA (United States)
- Science and Technology Facilities Council (STFC), Daresbury (United Kingdom). Daresbury Lab.
- 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)
- Univ. of California, Berkeley, CA (United States). Dept. of Chemistry, Dept. of Chemical and Biomolecular Engineering, and Dept. of Bioengineering
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22), Scientific User Facilities Division (SC-22.3 )
- OSTI Identifier:
- 1478341
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry
- Additional Journal Information:
- Journal Volume: 120; Journal Issue: 37; Journal ID: ISSN 1520-6106
- Publisher:
- American Chemical Society
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 97 MATHEMATICS AND COMPUTING
Citation Formats
Albaugh, Alex, Boateng, Henry A., Bradshaw, Richard T., Demerdash, Omar N., Dziedzic, Jacek, Mao, Yuezhi, Margul, Daniel T., Swails, Jason, Zeng, Qiao, Case, David A., Eastman, Peter, Wang, Lee-Ping, Essex, Jonathan W., Head-Gordon, Martin, Pande, Vijay S., Ponder, Jay W., Shao, Yihan, Skylaris, Chris-Kriton, Todorov, Ilian T., Tuckerman, Mark E., and Head-Gordon, Teresa. Advanced Potential Energy Surfaces for Molecular Simulation. United States: N. p., 2016.
Web. doi:10.1021/acs.jpcb.6b06414.
Albaugh, Alex, Boateng, Henry A., Bradshaw, Richard T., Demerdash, Omar N., Dziedzic, Jacek, Mao, Yuezhi, Margul, Daniel T., Swails, Jason, Zeng, Qiao, Case, David A., Eastman, Peter, Wang, Lee-Ping, Essex, Jonathan W., Head-Gordon, Martin, Pande, Vijay S., Ponder, Jay W., Shao, Yihan, Skylaris, Chris-Kriton, Todorov, Ilian T., Tuckerman, Mark E., & Head-Gordon, Teresa. Advanced Potential Energy Surfaces for Molecular Simulation. United States. https://doi.org/10.1021/acs.jpcb.6b06414
Albaugh, Alex, Boateng, Henry A., Bradshaw, Richard T., Demerdash, Omar N., Dziedzic, Jacek, Mao, Yuezhi, Margul, Daniel T., Swails, Jason, Zeng, Qiao, Case, David A., Eastman, Peter, Wang, Lee-Ping, Essex, Jonathan W., Head-Gordon, Martin, Pande, Vijay S., Ponder, Jay W., Shao, Yihan, Skylaris, Chris-Kriton, Todorov, Ilian T., Tuckerman, Mark E., and Head-Gordon, Teresa. Thu .
"Advanced Potential Energy Surfaces for Molecular Simulation". United States. https://doi.org/10.1021/acs.jpcb.6b06414. https://www.osti.gov/servlets/purl/1478341.
@article{osti_1478341,
title = {Advanced Potential Energy Surfaces for Molecular Simulation},
author = {Albaugh, Alex and Boateng, Henry A. and Bradshaw, Richard T. and Demerdash, Omar N. and Dziedzic, Jacek and Mao, Yuezhi and Margul, Daniel T. and Swails, Jason and Zeng, Qiao and Case, David A. and Eastman, Peter and Wang, Lee-Ping and Essex, Jonathan W. and Head-Gordon, Martin and Pande, Vijay S. and Ponder, Jay W. and Shao, Yihan and Skylaris, Chris-Kriton and Todorov, Ilian T. and Tuckerman, Mark E. and Head-Gordon, Teresa},
abstractNote = {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.},
doi = {10.1021/acs.jpcb.6b06414},
journal = {Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry},
number = 37,
volume = 120,
place = {United States},
year = {Thu Aug 11 00:00:00 EDT 2016},
month = {Thu Aug 11 00:00:00 EDT 2016}
}
Web of Science
Works referenced in this record:
Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n ‐Alkane Molecules
journal, December 1968
- Lifson, S.; Warshel, A.
- The Journal of Chemical Physics, Vol. 49, Issue 11
The Amber biomolecular simulation programs
journal, January 2005
- Case, David A.; Cheatham, Thomas E.; Darden, Tom
- Journal of Computational Chemistry, Vol. 26, Issue 16
CHARMM: The biomolecular simulation program
journal, July 2009
- Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.
- Journal of Computational Chemistry, Vol. 30, Issue 10
Scalable molecular dynamics with NAMD
journal, January 2005
- Phillips, James C.; Braun, Rosemary; Wang, Wei
- Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation
journal, November 2012
- Eastman, Peter; Friedrichs, Mark S.; Chodera, John D.
- Journal of Chemical Theory and Computation, Vol. 9, Issue 1
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
journal, June 1993
- Darden, Tom; York, Darrin; Pedersen, Lee
- The Journal of Chemical Physics, Vol. 98, Issue 12
Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations
journal, January 2004
- Sagui, Celeste; Pedersen, Lee G.; Darden, Thomas A.
- The Journal of Chemical Physics, Vol. 120, Issue 1
Simulating Hamiltonian Dynamics
journal, January 2009
- Leimkuhler, Benedict; Reich, Sebastian
- Cambridge University Press
Nosé–Hoover chains: The canonical ensemble via continuous dynamics
journal, August 1992
- Martyna, Glenn J.; Klein, Michael L.; Tuckerman, Mark
- The Journal of Chemical Physics, Vol. 97, Issue 4
Explicit reversible integrators for extended systems dynamics
journal, April 1996
- Martyna, Glenn J.; Tuckerman, Mark E.; Tobias, Douglas J.
- Molecular Physics, Vol. 87, Issue 5
The Role of Broken Symmetry in Solvation of a Spherical Cavity in Classical and Quantum Water Models
journal, July 2014
- Remsing, Richard C.; Baer, Marcel D.; Schenter, Gregory K.
- The Journal of Physical Chemistry Letters, Vol. 5, Issue 16
Ions at Aqueous Interfaces: From Water Surface to Hydrated Proteins
journal, May 2008
- Jungwirth, Pavel; Winter, Bernd
- Annual Review of Physical Chemistry, Vol. 59, Issue 1
Ions at Hydrophobic Aqueous Interfaces: Molecular Dynamics with Effective Polarization
journal, July 2012
- Vazdar, Mario; Pluhařová, Eva; Mason, Phil E.
- The Journal of Physical Chemistry Letters, Vol. 3, Issue 15
Calculations of the Electric Fields in Liquid Solutions
journal, November 2013
- Fried, Stephen D.; Wang, Lee-Ping; Boxer, Steven G.
- The Journal of Physical Chemistry B, Vol. 117, Issue 50
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
- Thompson, Mark A.; Schenter, Gregory K.
- The Journal of Physical Chemistry, Vol. 99, Issue 17
Optimizing Solute–Water van der Waals Interactions To Reproduce Solvation Free Energies
journal, April 2012
- Nerenberg, Paul S.; Jo, Brian; So, Clare
- The Journal of Physical Chemistry B, Vol. 116, Issue 15
Optimizing Protein−Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides
journal, March 2011
- Nerenberg, Paul S.; Head-Gordon, Teresa
- Journal of Chemical Theory and Computation, Vol. 7, Issue 4
Hydration Water Dynamics Near Biological Interfaces
journal, December 2008
- Johnson, Margaret E.; Malardier-Jugroot, Cecile; Murarka, Rajesh K.
- The Journal of Physical Chemistry B, Vol. 113, Issue 13
Effects of co-solvents on peptide hydration water structure and dynamics
journal, January 2010
- Johnson, Margaret E.; Malardier-Jugroot, Cecile; Head-Gordon, Teresa
- Phys. Chem. Chem. Phys., Vol. 12, Issue 2
Advanced Potential Energy Surfaces for Condensed Phase Simulation
journal, April 2014
- Demerdash, Omar; Yap, Eng-Hui; Head-Gordon, Teresa
- Annual Review of Physical Chemistry, Vol. 65, Issue 1
Incorporating electric polarizabilities in water-water interaction potentials
journal, January 1990
- Kuwajima, Satoru.; Warshel, Arieh.
- The Journal of Physical Chemistry, Vol. 94, Issue 1
An effective fragment method for modeling solvent effects in quantum mechanical calculations
journal, August 1996
- Day, Paul N.; Jensen, Jan H.; Gordon, Mark S.
- The Journal of Chemical Physics, Vol. 105, Issue 5
Toward a Molecular Orbital Derived Empirical Potential for Liquid Simulations
journal, January 1997
- Gao, Jiali
- The Journal of Physical Chemistry B, Vol. 101, Issue 4
Fluctuating Charge, Polarizable Dipole, and Combined Models: Parameterization from ab Initio Quantum Chemistry
journal, June 1999
- Stern, Harry A.; Kaminski, George A.; Banks, Jay L.
- The Journal of Physical Chemistry B, Vol. 103, Issue 22
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
- Cieplak, Piotr; Caldwell, James; Kollman, Peter
- Journal of Computational Chemistry, Vol. 22, Issue 10
Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests
journal, October 2002
- Kaminski, George A.; Stern, Harry A.; Berne, B. J.
- Journal of Computational Chemistry, Vol. 23, Issue 16
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations
journal, October 2002
- Ren, Pengyu; Ponder, Jay W.
- Journal of Computational Chemistry, Vol. 23, Issue 16
A simple polarizable model of water based on classical Drude oscillators
journal, September 2003
- Lamoureux, Guillaume; MacKerell, Alexander D.; Roux, Benoı̂t
- The Journal of Chemical Physics, Vol. 119, Issue 10
Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF
journal, December 2003
- Piquemal, Jean-Philip; Williams-Hubbard, Ben; Fey, Natalie
- Journal of Computational Chemistry, Vol. 24, Issue 16
Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from ab Initio Quantum Chemistry
journal, January 2004
- Kaminski, George A.; Stern, Harry A.; Berne, B. J.
- The Journal of Physical Chemistry A, Vol. 108, Issue 4
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
journal, January 2003
- Patel, Sandeep; Brooks, Charles L.
- Journal of Computational Chemistry, Vol. 25, Issue 1
A quantum mechanical polarizable force field for biomolecular interactions
journal, May 2005
- Donchev, A. G.; Ozrin, V. D.; Subbotin, M. V.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 22
Efficient Simulation Method for Polarizable Protein Force Fields: Application to the Simulation of BPTI in Liquid Water
journal, December 2004
- Harder, Edward; Kim, Byungchan; Friesner, Richard A.
- Journal of Chemical Theory and Computation, Vol. 1, Issue 1
Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides
journal, January 2006
- Wang, Zhi-Xiang; Zhang, Wei; Wu, Chun
- Journal of Computational Chemistry, Vol. 27, Issue 6
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
- Fanourgakis, George S.; Xantheas, Sotiris S.
- The Journal of Chemical Physics, Vol. 124, Issue 17
Virial Coefficients of Polarizable Water: Applications to Thermodynamic Properties and Molecular Clustering †
journal, November 2007
- Benjamin, Kenneth M.; Schultz, Andrew J.; Kofke, David A.
- The Journal of Physical Chemistry C, Vol. 111, Issue 43
Force field modeling of conformational energies: Importance of multipole moments and intramolecular polarization
journal, January 2007
- Rasmussen, Thomas D.; Ren, Pengyu; Ponder, Jay W.
- International Journal of Quantum Chemistry, Vol. 107, Issue 6
Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand−Macromolecule Complexes. A Bottom-Up Strategy
journal, October 2007
- Gresh, Nohad; Cisneros, G. Andrés; Darden, Thomas A.
- Journal of Chemical Theory and Computation, Vol. 3, Issue 6
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
- Geerke, Daan P.; van Gunsteren, Wilfred F.
- The Journal of Physical Chemistry B, Vol. 111, Issue 23
Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion
journal, October 2007
- Jorgensen, William L.; Jensen, Kasper P.; Alexandrova, Anastassia N.
- Journal of Chemical Theory and Computation, Vol. 3, Issue 6
Polarizabilities of individual molecules and ions in liquids from first principles
journal, November 2008
- Salanne, M.; Vuilleumier, R.; Madden, P. A.
- Journal of Physics: Condensed Matter, Vol. 20, Issue 49
Polarization effects in molecular mechanical force fields
journal, July 2009
- Cieplak, Piotr; Dupradeau, François-Yves; Duan, Yong
- Journal of Physics: Condensed Matter, Vol. 21, Issue 33
Exploring Ion Permeation Energetics in Gramicidin A Using Polarizable Charge Equilibration Force Fields
journal, September 2009
- Patel, Sandeep; Davis, Joseph E.; Bauer, Brad A.
- Journal of the American Chemical Society, Vol. 131, Issue 39
Accurate Intermolecular Potentials with Physically Grounded Electrostatics
journal, May 2011
- Tafipolsky, Maxim; Engels, Bernd
- Journal of Chemical Theory and Computation, Vol. 7, Issue 6
Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data
journal, November 2012
- Wang, Lee-Ping; Chen, Jiahao; Van Voorhis, Troy
- Journal of Chemical Theory and Computation, Vol. 9, Issue 1
Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
journal, November 2013
- Lopes, Pedro E. M.; Huang, Jing; Shim, Jihyun
- Journal of Chemical Theory and Computation, Vol. 9, Issue 12
i-TTM Model for Ab Initio-Based Ion–Water Interaction Potentials. 1. Halide–Water Potential Energy Functions
journal, November 2015
- Arismendi-Arrieta, Daniel J.; Riera, Marc; Bajaj, Pushp
- The Journal of Physical Chemistry B, Vol. 120, Issue 8
Calcium Binding to Calmodulin by Molecular Dynamics with Effective Polarization
journal, November 2014
- Kohagen, Miriam; Lepšík, Martin; Jungwirth, Pavel
- The Journal of Physical Chemistry Letters, Vol. 5, Issue 22
Accounting for Electronic Polarization Effects in Aqueous Sodium Chloride via Molecular Dynamics Aided by Neutron Scattering
journal, July 2015
- Kohagen, Miriam; Mason, Philip E.; Jungwirth, Pavel
- The Journal of Physical Chemistry B, Vol. 120, Issue 8
Evaluation of charge penetration between distributed multipolar expansions
journal, May 2000
- Freitag, Mark A.; Gordon, Mark S.; Jensen, Jan H.
- The Journal of Chemical Physics, Vol. 112, Issue 17
Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles
journal, January 2016
- Narth, Christophe; Lagardère, Louis; Polack, Étienne
- Journal of Computational Chemistry, Vol. 37, Issue 5
General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field
journal, May 2015
- Wang, Qiantao; Rackers, Joshua A.; He, Chenfeng
- Journal of Chemical Theory and Computation, Vol. 11, Issue 6
The effects of charge transfer on the properties of liquid water
journal, May 2011
- Lee, Alexis J.; Rick, Steven W.
- The Journal of Chemical Physics, Vol. 134, Issue 18
Charge Transfer Models of Zinc and Magnesium in Water
journal, March 2015
- Soniat, Marielle; Hartman, Lisa; Rick, Steven W.
- Journal of Chemical Theory and Computation, Vol. 11, Issue 4
Hydrated proton and hydroxide charge transfer at the liquid/vapor interface of water
journal, July 2015
- Soniat, Marielle; Kumar, Revati; Rick, Steven W.
- The Journal of Chemical Physics, Vol. 143, Issue 4
Ion association in aqueous solution
journal, January 2016
- Soniat, Marielle; Pool, Grayson; Franklin, Lisette
- Fluid Phase Equilibria, Vol. 407
The effects of charge transfer on the aqueous solvation of ions
journal, July 2012
- Soniat, Marielle; Rick, Steven W.
- The Journal of Chemical Physics, Vol. 137, Issue 4
Charge transfer effects of ions at the liquid water/vapor interface
journal, May 2014
- Soniat, Marielle; Rick, Steven W.
- The Journal of Chemical Physics, Vol. 140, Issue 18
Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation
journal, May 2003
- Ren, Pengyu; Ponder, Jay W.
- The Journal of Physical Chemistry B, Vol. 107, Issue 24
Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules
journal, August 2011
- Ren, Pengyu; Wu, Chuanjie; Ponder, Jay W.
- Journal of Chemical Theory and Computation, Vol. 7, Issue 10
Current Status of the AMOEBA Polarizable Force Field
journal, March 2010
- Ponder, Jay W.; Wu, Chuanjie; Ren, Pengyu
- The Journal of Physical Chemistry B, Vol. 114, Issue 8
Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals
journal, March 2011
- Schnieders, Michael J.; Fenn, Timothy D.; Pande, Vijay S.
- Journal of Chemical Theory and Computation, Vol. 7, Issue 4
Reversible multiple time scale molecular dynamics
journal, August 1992
- Tuckerman, M.; Berne, B. J.; Martyna, G. J.
- The Journal of Chemical Physics, Vol. 97, Issue 3
Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning
journal, March 2015
- Hopkins, Chad W.; Le Grand, Scott; Walker, Ross C.
- Journal of Chemical Theory and Computation, Vol. 11, Issue 4
Systematic Improvement of a Classical Molecular Model of Water
journal, August 2013
- Wang, Lee-Ping; Head-Gordon, Teresa; Ponder, Jay W.
- The Journal of Physical Chemistry B, Vol. 117, Issue 34
Convergence of the Many-Body Expansion for Energy and Forces for Classical Polarizable Models in the Condensed Phase
journal, July 2016
- Demerdash, Omar; Head-Gordon, Teresa
- Journal of Chemical Theory and Computation, Vol. 12, Issue 8
Introducing ONETEP : Linear-scaling density functional simulations on parallel computers
journal, February 2005
- Skylaris, Chris-Kriton; Haynes, Peter D.; Mostofi, Arash A.
- The Journal of Chemical Physics, Vol. 122, Issue 8
Advances in molecular quantum chemistry contained in the Q-Chem 4 program package
journal, September 2014
- Shao, Yihan; Gan, Zhengting; Epifanovsky, Evgeny
- Molecular Physics, Vol. 113, Issue 2
An efficient and stable hybrid extended Lagrangian/self-consistent field scheme for solving classical mutual induction
journal, November 2015
- Albaugh, Alex; Demerdash, Omar; Head-Gordon, Teresa
- The Journal of Chemical Physics, Vol. 143, Issue 17
A Stochastic, Resonance-Free Multiple Time-Step Algorithm for Polarizable Models That Permits Very Large Time Steps
journal, April 2016
- Margul, Daniel T.; Tuckerman, Mark E.
- Journal of Chemical Theory and Computation, Vol. 12, Issue 5
Arbitrary order permanent Cartesian multipolar electrostatic interactions
journal, January 2015
- Boateng, H. A.; Todorov, I. T.
- The Journal of Chemical Physics, Vol. 142, Issue 3
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
- Mao, Yuezhi; Horn, Paul R.; Mardirossian, Narbe
- The Journal of Chemical Physics, Vol. 145, Issue 4
Water Molecule Interactions
journal, December 1970
- Hankins, D.; Moskowitz, J. W.; Stillinger, F. H.
- The Journal of Chemical Physics, Vol. 53, Issue 12
Electrostatically embedded many-body method for dipole moments, partial atomic charges, and charge transfer
journal, January 2012
- Leverentz, Hannah R.; Maerzke, Katie A.; Keasler, Samuel J.
- Physical Chemistry Chemical Physics, Vol. 14, Issue 21
A generalized many-body expansion and a unified view of fragment-based methods in electronic structure theory
journal, August 2012
- Richard, Ryan M.; Herbert, John M.
- The Journal of Chemical Physics, Vol. 137, Issue 6
Fragmentation Methods: A Route to Accurate Calculations on Large Systems
journal, August 2011
- Gordon, Mark S.; Fedorov, Dmitri G.; Pruitt, Spencer R.
- Chemical Reviews, Vol. 112, Issue 1
Building Force Fields: An Automatic, Systematic, and Reproducible Approach
journal, May 2014
- Wang, Lee-Ping; Martinez, Todd J.; Pande, Vijay S.
- The Journal of Physical Chemistry Letters, Vol. 5, Issue 11
Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model
journal, September 2014
- Laury, Marie L.; Wang, Lee-Ping; Pande, Vijay S.
- The Journal of Physical Chemistry B, Vol. 119, Issue 29
Nonorthogonal generalized Wannier function pseudopotential plane-wave method
journal, July 2002
- Skylaris, Chris-Kriton; Mostofi, Arash A.; Haynes, Peter D.
- Physical Review B, Vol. 66, Issue 3
Biomolecular electrostatics and solvation: a computational perspective
journal, November 2012
- Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G.
- Quarterly Reviews of Biophysics, Vol. 45, Issue 4
Distributed Multipole Analysis: Stability for Large Basis Sets
journal, September 2005
- Stone, Anthony J.
- Journal of Chemical Theory and Computation, Vol. 1, Issue 6
Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in O NETEP
journal, June 2015
- Vitale, Valerio; Dziedzic, Jacek; Dubois, Simon M. -M.
- Journal of Chemical Theory and Computation, Vol. 11, Issue 7
Electrostatic considerations affecting the calculated HOMO–LUMO gap in protein molecules
journal, March 2013
- Lever, Greg; Cole, Daniel J.; Hine, Nicholas D. M.
- Journal of Physics: Condensed Matter, Vol. 25, Issue 15
LIBEFP: A new parallel implementation of the effective fragment potential method as a portable software library
journal, July 2013
- Kaliman, Ilya A.; Slipchenko, Lyudmila V.
- Journal of Computational Chemistry, Vol. 34, Issue 26
Effective fragment potential method in Q-CHEM : A guide for users and developers : Software News and Updates
journal, January 2013
- Ghosh, Debashree; Kosenkov, Dmytro; Vanovschi, Vitalii
- Journal of Computational Chemistry, Vol. 34, Issue 12
A smooth particle mesh Ewald method
journal, November 1995
- Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L.
- The Journal of Chemical Physics, Vol. 103, Issue 19
An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald
journal, May 2014
- Simmonett, Andrew C.; Pickard, Frank C.; Schaefer, Henry F.
- The Journal of Chemical Physics, Vol. 140, Issue 18
Psi4: an open-source ab initio electronic structure program : Psi4: an electronic structure program
journal, October 2011
- Turney, Justin M.; Simmonett, Andrew C.; Parrish, Robert M.
- Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 4
NWChem: scalable parallel computational chemistry: NWChem
journal, May 2011
- van Dam, H. J. J.; de Jong, W. A.; Bylaska, E.
- Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 1, Issue 6
Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method
journal, December 2002
- Das, Debananda; Eurenius, Kirsten P.; Billings, Eric M.
- The Journal of Chemical Physics, Vol. 117, Issue 23
Fast evaluation of polarizable forces
journal, October 2005
- Wang, Wei; Skeel, Robert D.
- The Journal of Chemical Physics, Vol. 123, Issue 16
Convergence acceleration of iterative sequences. the case of scf iteration
journal, July 1980
- Pulay, Péter
- Chemical Physics Letters, Vol. 73, Issue 2
Molecular dynamics simulation of polarizable water by an extended Lagrangian method
journal, October 1992
- Van Belle, Daniel; Froeyen, Matheus; Lippens, Guy
- Molecular Physics, Vol. 77, Issue 2
Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm
journal, August 2003
- Lamoureux, Guillaume; Roux, Benoı̂t
- The Journal of Chemical Physics, Vol. 119, Issue 6
Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications
journal, August 2009
- Lopes, Pedro E. M.; Roux, Benoit; MacKerell, Alexander D.
- Theoretical Chemistry Accounts, Vol. 124, Issue 1-2
Efficient treatment of induced dipoles
journal, August 2015
- Simmonett, Andrew C.; Pickard, Frank C.; Shao, Yihan
- The Journal of Chemical Physics, Vol. 143, Issue 7
Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations
journal, March 2014
- Lipparini, Filippo; Lagardère, Louis; Stamm, Benjamin
- Journal of Chemical Theory and Computation, Vol. 10, Issue 4
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
- Lagardère, Louis; Lipparini, Filippo; Polack, Étienne
- Journal of Chemical Theory and Computation, Vol. 11, Issue 6
Extended Born-Oppenheimer Molecular Dynamics
journal, March 2008
- Niklasson, Anders M. N.
- Physical Review Letters, Vol. 100, Issue 12
Generalized extended Lagrangian Born-Oppenheimer molecular dynamics
journal, October 2014
- Niklasson, Anders M. N.; Cawkwell, Marc J.
- The Journal of Chemical Physics, Vol. 141, Issue 16
Extended Lagrangian Born–Oppenheimer molecular dynamics with dissipation
journal, June 2009
- Niklasson, Anders M. N.; Steneteg, Peter; Odell, Anders
- The Journal of Chemical Physics, Vol. 130, Issue 21
Time-reversible ab initio molecular dynamics
journal, April 2007
- Niklasson, Anders M. N.; Tymczak, C. J.; Challacombe, Matt
- The Journal of Chemical Physics, Vol. 126, Issue 14
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
- Swope, William C.; Andersen, Hans C.; Berens, Peter H.
- The Journal of Chemical Physics, Vol. 76, Issue 1
Molecular dynamics with coupling to an external bath
journal, October 1984
- Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.
- The Journal of Chemical Physics, Vol. 81, Issue 8
Integrating the Car–Parrinello equations. I. Basic integration techniques
journal, July 1994
- Tuckerman, Mark E.; Parrinello, Michele
- The Journal of Chemical Physics, Vol. 101, Issue 2
Long Time Molecular Dynamics for Enhanced Conformational Sampling in Biomolecular Systems
journal, October 2004
- Minary, P.; Tuckerman, M. E.; Martyna, G. J.
- Physical Review Letters, Vol. 93, Issue 15
Stochastic, resonance-free multiple time-step algorithm for molecular dynamics with very large time steps
journal, December 2013
- Leimkuhler, Ben; Margul, Daniel T.; Tuckerman, Mark E.
- Molecular Physics, Vol. 111, Issue 22-23
DL_MULTI—A molecular dynamics program to use distributed multipole electrostatic models to simulate the dynamics of organic crystals
journal, June 2008
- Leslie, M.
- Molecular Physics, Vol. 106, Issue 12
DL_POLY_3: new dimensions in molecular dynamics simulations via massive parallelism
journal, January 2006
- Todorov, Ilian T.; Smith, William; Trachenko, Kostya
- Journal of Materials Chemistry, Vol. 16, Issue 20, p. 1911-1918
Ewald summation and reaction field methods for potentials with atomic charges, dipoles, and polarizabilities
journal, April 2000
- Nymand, Thomas M.; Linse, Per
- The Journal of Chemical Physics, Vol. 112, Issue 14
Direct Wolf summation of a polarizable force field for silica
journal, May 2010
- Brommer, Peter; Beck, Philipp; Chatzopoulos, Andreas
- The Journal of Chemical Physics, Vol. 132, Issue 19
A DAFT DL_POLY distributed memory adaptation of the Smoothed Particle Mesh Ewald method
journal, September 2006
- Bush, I. J.; Todorov, I. T.; Smith, W.
- Computer Physics Communications, Vol. 175, Issue 5
Generalized Gradient Approximation Made Simple
journal, October 1996
- Perdew, John P.; Burke, Kieron; Ernzerhof, Matthias
- Physical Review Letters, Vol. 77, Issue 18, p. 3865-3868
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
journal, April 2010
- Grimme, Stefan; Antony, Jens; Ehrlich, Stephan
- The Journal of Chemical Physics, Vol. 132, Issue 15
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
- Mardirossian, Narbe; Head-Gordon, Martin
- Physical Chemistry Chemical Physics, Vol. 16, Issue 21
Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V
journal, February 2015
- Mardirossian, Narbe; Head-Gordon, Martin
- The Journal of Chemical Physics, Vol. 142, Issue 7
Property-optimized Gaussian basis sets for molecular response calculations
journal, October 2010
- Rappoport, Dmitrij; Furche, Filipp
- The Journal of Chemical Physics, Vol. 133, Issue 13
Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit
journal, April 2007
- Lee, Hee-Seung; Tuckerman, Mark E.
- The Journal of Chemical Physics, Vol. 126, Issue 16
Structure of liquid water at ambient temperature from ab initio molecular dynamics performed in the complete basis set limit
journal, October 2006
- Lee, Hee-Seung; Tuckerman, Mark E.
- The Journal of Chemical Physics, Vol. 125, Issue 15
Ab initio molecular dynamics study of water at constant pressure using converged basis sets and empirical dispersion corrections
journal, July 2012
- Ma, Zhonghua; Zhang, Yanli; Tuckerman, Mark E.
- The Journal of Chemical Physics, Vol. 137, Issue 4
On the connection between proton transport, structural diffusion, and reorientation of the hydrated hydroxide ion as a function of temperature
journal, August 2011
- Ma, Zhonghua; Tuckerman, Mark E.
- Chemical Physics Letters, Vol. 511, Issue 4-6
Ab Initio Molecular Dynamics Study of the Aqueous HOO – Ion
journal, April 2014
- Ma, Zhonghua; Anick, David; Tuckerman, Mark E.
- The Journal of Physical Chemistry B, Vol. 118, Issue 28
Concerted Hydrogen-Bond Dynamics in the Transport Mechanism of the Hydrated Proton: A First-Principles Molecular Dynamics Study
journal, November 2009
- Berkelbach, Timothy C.; Lee, Hee-Seung; Tuckerman, Mark E.
- Physical Review Letters, Vol. 103, Issue 23
Ab Initio Molecular Dynamics with Discrete Variable Representation Basis Sets: Techniques and Application to Liquid Water †
journal, April 2006
- Lee, Hee-Seung; Tuckerman, Mark E.
- The Journal of Physical Chemistry A, Vol. 110, Issue 16
Auxiliary basis sets to approximate Coulomb potentials
journal, June 1995
- Eichkorn, Karin; Treutler, Oliver; Öhm, Holger
- Chemical Physics Letters, Vol. 240, Issue 4
An implementation of RI-SCF on parallel computers
journal, January 1997
- Fr�chtl, Herbert A.; Kendall, Rick A.; Harrison, Robert J.
- International Journal of Quantum Chemistry, Vol. 64, Issue 1
Fast, accurate evaluation of exact exchange: The occ-RI-K algorithm
journal, July 2015
- Manzer, Samuel; Horn, Paul R.; Mardirossian, Narbe
- The Journal of Chemical Physics, Vol. 143, Issue 2
Efficient Implementation of the Pair Atomic Resolution of the Identity Approximation for Exact Exchange for Hybrid and Range-Separated Density Functionals
journal, January 2015
- Manzer, Samuel F.; Epifanovsky, Evgeny; Head-Gordon, Martin
- Journal of Chemical Theory and Computation, Vol. 11, Issue 2
Dual-basis second-order Møller-Plesset perturbation theory: A reduced-cost reference for correlation calculations
journal, August 2006
- Steele, Ryan P.; DiStasio, Robert A.; Shao, Yihan
- The Journal of Chemical Physics, Vol. 125, Issue 7
Non-Covalent Interactions with Dual-Basis Methods: Pairings for Augmented Basis Sets
journal, April 2009
- Steele, Ryan P.; DiStasio, Robert A.; Head-Gordon, Martin
- Journal of Chemical Theory and Computation, Vol. 5, Issue 6
The SAMPL4 host–guest blind prediction challenge: an overview
journal, March 2014
- Muddana, Hari S.; Fenley, Andrew T.; Mobley, David L.
- Journal of Computer-Aided Molecular Design, Vol. 28, Issue 4
Standard Free Energy of Releasing a Localized Water Molecule from the Binding Pockets of Proteins: Double-Decoupling Method
journal, June 2004
- Hamelberg, Donald; McCammon, J. Andrew
- Journal of the American Chemical Society, Vol. 126, Issue 24
Efficient estimation of free energy differences from Monte Carlo data
journal, October 1976
- Bennett, Charles H.
- Journal of Computational Physics, Vol. 22, Issue 2
Calculating binding free energies of host–guest systems using the AMOEBA polarizable force field
journal, January 2016
- Bell, David R.; Qi, Rui; Jing, Zhifeng
- Physical Chemistry Chemical Physics, Vol. 18, Issue 44
Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field
journal, July 2016
- Bradshaw, Richard T.; Essex, Jonathan W.
- Journal of Chemical Theory and Computation, Vol. 12, Issue 8
Why do molecules interact? The origin of electron donor-acceptor complexes, hydrogen bonding and proton affinity
journal, August 1977
- Morokuma, Keiji
- Accounts of Chemical Research, Vol. 10, Issue 8
Energy decomposition analysis: Energy decomposition analysis
journal, June 2011
- Hopffgarten, Moritz von; Frenking, Gernot
- Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 1
Energy decomposition analysis approaches and their evaluation on prototypical protein–drug interaction patterns
journal, January 2015
- Phipps, Maximillian J. S.; Fox, Thomas; Tautermann, Christofer S.
- Chemical Society Reviews, Vol. 44, Issue 10
Perturbation Theory Approach to Intermolecular Potential Energy Surfaces of van der Waals Complexes
journal, November 1994
- Jeziorski, Bogumil; Moszynski, Robert; Szalewicz, Krzysztof
- Chemical Reviews, Vol. 94, Issue 7
Wavefunction methods for noncovalent interactions: Noncovalent interactions
journal, July 2011
- Hohenstein, Edward G.; Sherrill, C. David
- Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 2
Symmetry-adapted perturbation theory of intermolecular forces: Symmetry-adapted perturbation theory
journal, August 2011
- Szalewicz, Krzysztof
- Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 2
A new energy decomposition scheme for molecular interactions within the Hartree-Fock approximation
journal, March 1976
- Kitaura, Kazuo; Morokuma, Keiji
- International Journal of Quantum Chemistry, Vol. 10, Issue 2
Energy decomposition analysis of intermolecular interactions using a block-localized wave function approach
journal, April 2000
- Mo, Yirong; Gao, Jiali; Peyerimhoff, Sigrid D.
- The Journal of Chemical Physics, Vol. 112, Issue 13
Block-Localized Wavefunction (BLW) Method at the Density Functional Theory (DFT) Level
journal, August 2007
- Mo, Yirong; Song, Lingchun; Lin, Yuchun
- The Journal of Physical Chemistry A, Vol. 111, Issue 34
Energy decomposition analysis based on a block-localized wavefunction and multistate density functional theory
journal, January 2011
- Mo, Yirong; Bao, Peng; Gao, Jiali
- Physical Chemistry Chemical Physics, Vol. 13, Issue 15
Unravelling the Origin of Intermolecular Interactions Using Absolutely Localized Molecular Orbitals
journal, September 2007
- Khaliullin, Rustam Z.; Cobar, Erika A.; Lochan, Rohini C.
- The Journal of Physical Chemistry A, Vol. 111, Issue 36
Analysis of charge transfer effects in molecular complexes based on absolutely localized molecular orbitals
journal, May 2008
- Khaliullin, Rustam Z.; Bell, Alexis T.; Head-Gordon, Martin
- The Journal of Chemical Physics, Vol. 128, Issue 18
Unrestricted absolutely localized molecular orbitals for energy decomposition analysis: Theory and applications to intermolecular interactions involving radicals
journal, April 2013
- Horn, Paul R.; Sundstrom, Eric Jon; Baker, Thomas A.
- The Journal of Chemical Physics, Vol. 138, Issue 13
Polarization contributions to intermolecular interactions revisited with fragment electric-field response functions
journal, September 2015
- Horn, Paul R.; Head-Gordon, Martin
- The Journal of Chemical Physics, Vol. 143, Issue 11
Alternative definitions of the frozen energy in energy decomposition analysis of density functional theory calculations
journal, February 2016
- Horn, Paul R.; Head-Gordon, Martin
- The Journal of Chemical Physics, Vol. 144, Issue 8
Defining the contributions of permanent electrostatics, Pauli repulsion, and dispersion in density functional theory calculations of intermolecular interaction energies
journal, March 2016
- Horn, Paul R.; Mao, Yuezhi; Head-Gordon, Martin
- The Journal of Chemical Physics, Vol. 144, Issue 11
Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism
journal, June 2014
- Camilloni, C.; Sahakyan, A. B.; Holliday, M. J.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 28
Insights into the catalytic mechanism of peptidyl prolyl cis/trans isomerases
journal, January 2004
- Fanghänel, Jörg
- Frontiers in Bioscience, Vol. 9, Issue 1-3
Describing Noncovalent Interactions beyond the Common Approximations: How Accurate Is the “Gold Standard,” CCSD(T) at the Complete Basis Set Limit?
journal, April 2013
- Řezáč, Jan; Hobza, Pavel
- Journal of Chemical Theory and Computation, Vol. 9, Issue 5
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
- Jurečka, Petr; Šponer, Jiří; Černý, Jiří
- Physical Chemistry Chemical Physics, Vol. 8, Issue 17, p. 1985-1993
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
- Marshall, Michael S.; Burns, Lori A.; Sherrill, C. David
- The Journal of Chemical Physics, Vol. 135, Issue 19
Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods
journal, December 2011
- Řezáč, Jan; Hobza, Pavel
- Journal of Chemical Theory and Computation, Vol. 8, Issue 1
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
- Lao, Ka Un; Herbert, John M.
- The Journal of Chemical Physics, Vol. 139, Issue 3
Accurate and Efficient Quantum Chemistry Calculations for Noncovalent Interactions in Many-Body Systems: The XSAPT Family of Methods
journal, December 2014
- Lao, Ka Un; Herbert, John M.
- The Journal of Physical Chemistry A, Vol. 119, Issue 2
Probing non-covalent interactions with a second generation energy decomposition analysis using absolutely localized molecular orbitals
journal, January 2016
- Horn, Paul R.; Mao, Yuezhi; Head-Gordon, Martin
- Physical Chemistry Chemical Physics, Vol. 18, Issue 33
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- Sharma, Gaurav; Hu, Qiaoyu; Jayasinghe-Arachchige, Vindi M.
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journal, October 2017
- Huang, Jing; Simmonett, Andrew C.; Pickard, Frank C.
- The Journal of Chemical Physics, Vol. 147, Issue 16
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journal, September 2019
- Pal, Rajat K.; Gallicchio, Emilio
- The Journal of Chemical Physics, Vol. 151, Issue 12
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journal, November 2018
- Krylov, Anna; Windus, Theresa L.; Barnes, Taylor
- The Journal of Chemical Physics, Vol. 149, Issue 18
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
- Hagler, A. T.
- Journal of Computer-Aided Molecular Design, Vol. 33, Issue 2
The strengths and limitations of effective centroid force models explored by studying isotopic effects in liquid water
journal, May 2018
- Yuan, Ying; Li, Jicun; Li, Xin-Zheng
- The Journal of Chemical Physics, Vol. 148, Issue 18
Molecular dynamics based enhanced sampling of collective variables with very large time steps
journal, January 2018
- Chen, Pei-Yang; Tuckerman, Mark E.
- The Journal of Chemical Physics, Vol. 148, Issue 2
Inertial extended-Lagrangian scheme for solving charge equilibration models
journal, January 2019
- Leven, Itai; Head-Gordon, Teresa
- Physical Chemistry Chemical Physics, Vol. 21, Issue 34
Natural selection based on coordination chemistry: computational assessment of [4Fe–4S]-maquettes with non-coded amino acids
journal, October 2019
- Szilagyi, Robert K.; Hanscam, Rebecca; Shepard, Eric M.
- Interface Focus, Vol. 9, Issue 6
Secondary structure analysis of peptides with relevance to iron–sulfur cluster nesting
journal, December 2018
- Hanscam, Rebecca; Shepard, Eric M.; Broderick, Joan B.
- Journal of Computational Chemistry, Vol. 40, Issue 2
Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity
journal, September 2018
- Huggins, David J.; Biggin, Philip C.; Dämgen, Marc A.
- Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 9, Issue 3
A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes
journal, October 2018
- König, Gerhard; Pickard, Frank; Huang, Jing
- Molecules, Vol. 23, Issue 10
Biomolecular simulations: from dynamics and mechanisms to computational assays of biological activity
text, January 2019
- Huggins, David
- Apollo - University of Cambridge Repository
Inertial Extended-Lagrangian Scheme for Solving Charge Equilibration Models
text, January 2019
- Leven, Itai; Head-Gordon, Teresa
- arXiv
A FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics
journal, November 2019
- Hughes, Zak E.; Ren, Emmanuel; Thacker, Joseph C. R.
- Journal of Computational Chemistry, Vol. 41, Issue 7
Convergence of stochastic-extended Lagrangian molecular dynamics method for polarizable force field simulation
journal, August 2021
- An, Dong; Cheng, Sara Y.; Head-Gordon, Teresa
- Journal of Computational Physics, Vol. 438
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journal, July 2017
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- PLOS Computational Biology, Vol. 13, Issue 7