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Poier PP, Lagardère L, Piquemal JP. Smooth particle mesh Ewald-integrated stochastic Lanczos many-body dispersion algorithm. J Chem Phys 2023; 159:154109. [PMID: 37861116 DOI: 10.1063/5.0166476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023] Open
Abstract
We derive and implement an alternative formulation of the Stochastic Lanczos algorithm to be employed in connection with the Many-Body Dispersion model (MBD). Indeed, this formulation, which is only possible due to the Stochastic Lanczos' reliance on matrix-vector products, introduces generalized dipoles and fields. These key quantities allow for a state-of-the-art treatment of periodic boundary conditions via the O(Nlog(N)) Smooth Particle Mesh Ewald (SPME) approach which uses efficient fast Fourier transforms. This SPME-Lanczos algorithm drastically outperforms the standard replica method which is affected by a slow and conditionally convergence rate that limits an efficient and reliable inclusion of long-range periodic boundary conditions interactions in many-body dispersion modelling. The proposed algorithm inherits the embarrassingly parallelism of the original Stochastic Lanczos scheme, thus opening up for a fully converged and efficient periodic boundary conditions treatment of MBD approaches.
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Affiliation(s)
- Pier Paolo Poier
- Laboratoire de Chimie Théorique, Sorbonne Université, 75005 Paris, France
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, Sorbonne Université, 75005 Paris, France
- Sorbonne Université, IP2CT, FR 2622 CNRS, Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Université, 75005 Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
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Corrigan RA, Thiel AC, Lynn JR, Casavant TL, Ren P, Ponder JW, Schnieders MJ. A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model. J Chem Phys 2023; 159:054102. [PMID: 37526158 PMCID: PMC10396400 DOI: 10.1063/5.0158914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023] Open
Abstract
Computational simulation of biomolecules can provide important insights into protein design, protein-ligand binding interactions, and ab initio biomolecular folding, among other applications. Accurate treatment of the solvent environment is essential in such applications, but the use of explicit solvents can add considerable cost. Implicit treatment of solvent effects using a dielectric continuum model is an attractive alternative to explicit solvation since it is able to describe solvation effects without the inclusion of solvent degrees of freedom. Previously, we described the development and parameterization of implicit solvent models for small molecules. Here, we extend the parameterization of the generalized Kirkwood (GK) implicit solvent model for use with biomolecules described by the AMOEBA force field via the addition of corrections to the calculation of effective radii that account for interstitial spaces that arise within biomolecules. These include element-specific pairwise descreening scale factors, a short-range neck contribution to describe the solvent-excluded space between pairs of nearby atoms, and finally tanh-based rescaling of the overall descreening integral. We then apply the AMOEBA/GK implicit solvent to a set of ten proteins and achieve an average coordinate root mean square deviation for the experimental structures of 2.0 Å across 500 ns simulations. Overall, the continued development of implicit solvent models will help facilitate the simulation of biomolecules on mechanistically relevant timescales.
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Affiliation(s)
- Rae A. Corrigan
- Roy J. Carver Department of Biomedical Engineering, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Andrew C. Thiel
- Roy J. Carver Department of Biomedical Engineering, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Jack R. Lynn
- Roy J. Carver Department of Biomedical Engineering, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Thomas L. Casavant
- Department of Electrical and Computer Engineering, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas in Austin, Austin, Texas 78712, USA
| | - Jay W. Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
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Poier PP. Variational Formulation of the Bond Capacity Charge Polarization Model. J Chem Phys 2022; 156:104101. [DOI: 10.1063/5.0082680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Corrigan RA, Qi G, Thiel AC, Lynn JR, Walker BD, Casavant TL, Lagardere L, Piquemal JP, Ponder JW, Ren P, Schnieders MJ. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. J Chem Theory Comput 2021; 17:2323-2341. [PMID: 33769814 DOI: 10.1021/acs.jctc.0c01286] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Computational protein design, ab initio protein/RNA folding, and protein-ligand screening can be too computationally demanding for explicit treatment of solvent. For these applications, implicit solvent offers a compelling alternative, which we describe here for the polarizable atomic multipole AMOEBA force field based on three treatments of continuum electrostatics: numerical solutions to the nonlinear and linearized versions of the Poisson-Boltzmann equation (PBE), the domain-decomposition conductor-like screening model (ddCOSMO) approximation to the PBE, and the analytic generalized Kirkwood (GK) approximation. The continuum electrostatics models are combined with a nonpolar estimator based on novel cavitation and dispersion terms. Electrostatic model parameters are numerically optimized using a least-squares style target function based on a library of 103 small-molecule solvation free energy differences. Mean signed errors for the adaptive Poisson-Boltzmann solver (APBS), ddCOSMO, and GK models are 0.05, 0.00, and 0.00 kcal/mol, respectively, while the mean unsigned errors are 0.70, 0.63, and 0.58 kcal/mol, respectively. Validation of the electrostatic response of the resulting implicit solvents, which are available in the Tinker (or Tinker-HP), OpenMM, and Force Field X software packages, is based on comparisons to explicit solvent simulations for a series of proteins and nucleic acids. Overall, the emergence of performative implicit solvent models for polarizable force fields opens the door to their use for folding and design applications.
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Affiliation(s)
- Rae A Corrigan
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Guowei Qi
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Andrew C Thiel
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Jack R Lynn
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Brandon D Walker
- Department of Biomedical Engineering, University of Texas in Austin, Austin, Texas 78712, United States
| | - Thomas L Casavant
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States
| | - Louis Lagardere
- Department of Chemistry, Sorbonne Université, F-75005 Paris, France
| | | | - Jay W Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas in Austin, Austin, Texas 78712, United States
| | - Michael J Schnieders
- Roy J Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, United States.,Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
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Nottoli M, Lipparini F. General formulation of polarizable embedding models and of their coupling. J Chem Phys 2020; 153:224108. [PMID: 33317291 DOI: 10.1063/5.0035165] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Univeristà di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Univeristà di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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Oliveira MP, Andrey M, Rieder SR, Kern L, Hahn DF, Riniker S, Horta BAC, Hünenberger PH. Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes. J Chem Theory Comput 2020; 16:7525-7555. [DOI: 10.1021/acs.jctc.0c00683] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Maurice Andrey
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R. Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Leyla Kern
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - David F. Hahn
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
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Poier PP, Jensen F. Polarizable charges in a generalized Born reaction potential. J Chem Phys 2020; 153:024111. [DOI: 10.1063/5.0012022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Pier Paolo Poier
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
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Poier PP, Lagardère L, Piquemal JP, Jensen F. Molecular Dynamics Using Nonvariational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation, and Application to the Bond Capacity Model. J Chem Theory Comput 2019; 15:6213-6224. [DOI: 10.1021/acs.jctc.9b00721] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Pier Paolo Poier
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Louis Lagardère
- Sorbonne Université, Institut Parisien de Chimie Physique et Théorique, 75005, Paris, France
- Sorbonne Université, Institut des Sciences du Calcul et des Données, 75005, Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, 75005, Paris, France
- Sorbonne Université, Institut Universitaire de France, 75005, Paris, France
- University of Texas, Department of Biomedical Engineering, Austin, Texas, United States
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
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