Polarizable charges in a generalized Born reaction potential

Poier, Pier Paolo; Jensen, Frank

doi:10.1063/5.0012022

Cited by 6 publications

(5 citation statements)

References 64 publications

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“…The application of the DIIS together with fixed-point iterative methods in solving linear systems of equations makes the overall procedure equivalent to the generalized minimal residual method (GMRES), which, belonging to the Krylov subspace class of iterative methods, is known for its fast and robust convergence properties . We mention that the coupled fixed-point/DIIS iterative schemes have proven successful in the context of modeling many-body polarization interactions, − and this motivates the use of this mixed procedure in the solution of eq .…”

Section: Theorymentioning

confidence: 99%

O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems

Poier¹,

Lagardère²,

Piquemal

2022

J. Chem. Theory Comput.

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We propose a new strategy to solve the key equations of the many-body dispersion (MBD) model by Tkatchenko, DiStasio Jr., and Ambrosetti. Our approach overcomes the original computational complexity that limits its applicability to large molecular systems within the context of density functional theory. First, to generate the required frequency-dependent screened polarizabilities, we introduce an efficient solution to the Dyson-like self-consistent screening equations. The scheme reduces the number of variables and, coupled to a direct inversion of the iterative subspace extrapolation, exhibits linear-scaling performances. Second, we apply a stochastic Lanczos trace estimator resolution to the equations evaluating the many-body interaction energy of coupled quantum harmonic oscillators. While scaling linearly, it also enables communication-free pleasingly parallel implementations. As the resulting stochastic massively parallel MBD approach is found to exhibit minimal memory requirements, it opens up the possibility of computing accurate many-body van der Waals interactions of millions-atoms’ complex materials and solvated biosystems with computational times in the range of minutes.

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Section: Theorymentioning

confidence: 99%

O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems

Poier¹,

Lagardère²,

Piquemal

2022

J. Chem. Theory Comput.

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“…Similarly, the AMOEBA force field for proteins 29 and nucleic acids 30 has been combined with PB 6,8 , ddCOSMO 31 , and GK 12,32 electrostatic continuum models. More recently, the Drude oscillator polarizable force field [33][34][35][36][37][38][39][40][41][42][43][44][45][46][47] has been combined with PB electrostatics and used to study pKa shifts 48,49 .…”

Section: Introductionmentioning

confidence: 99%

A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model

Corrigan

Thiel

Lynn

et al. 2023

The Journal of Chemical Physics

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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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“…For the BC-GB model, NVE molecular dynamics was shown to conserve energy at a modest increase in cost of only 15% relative to vacuum 53 . Although beyond our focus on implicit solvents for biomolecular polarizable force fields, there is a large body of work dedicated to quantum mechanical SCRF implicit solvents [54][55][56] , including the Polarizable Continuum Model (PCM) 57,58 , the Solvent Model (SM) series [59][60][61] , and Conductor-like Screening Models (COSMO) 62,63 .…”

Section: Introductionmentioning

confidence: 99%

“…A second recent example combined the bond capacity (BC) polarization model with both the generalized Born (GB) model and the conductor-like polarizable continuum model (C-PCM) . For the BC–GB model, NVE molecular dynamics (MD) was shown to conserve energy at a modest increase in cost of only 15% relative to vacuum . Cooper et al have developed an electrostatics solver called PyGBe, which employs a tree-code accelerated boundary-element formulation.…”

Section: Introductionmentioning

confidence: 99%

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

Corrigan

Thiel

et al. 2021

J. Chem. Theory Comput.

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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 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 electrostatic 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 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 0.51 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 will open the door to their use for folding and design applications.

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Polarizable charges in a generalized Born reaction potential

Cited by 6 publications

References 64 publications

O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems

O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems

A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

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