Time-reversible always stable predictor-corrector method for molecular dynamics of polarizable molecules (original) (raw)
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A current emphasis in empirical force fields is on the development of potential functions that explicitly treat electronic polarizability. In the present article, the commonly used methodologies for modeling electronic polarization are presented along with an overview of selected application studies. Models presented include induced point-dipoles, classical Drude oscillators, and fluctuating charge methods. The theoretical background of each method is followed by an introduction to extended Lagrangian integrators required for computationally tractable molecular dynamics simulations using polarizable force fields. The remainder of the review focuses on application studies using these methods. Emphasis is placed on water models, for which numerous examples exist, with a more thorough discussion presented on the recently published models associated with the Drude-based CHARMM and the AMOEBA force fields. The utility of polarizable models for the study of ion solvation is then presented followed by an overview of studies of small molecules (e.g., CCl 4 , alkanes, etc.) and macromolecule (proteins, nucleic acids and lipid bilayers) application studies. The review is written with the goal of providing a general overview of the current status of the field and to facilitate future application and developments.
A current emphasis in empirical force fields is on the development of potential functions that explicitly treat electronic polarizability. In the present article, the commonly used methodologies for modeling electronic polarization are presented along with an overview of selected application studies. Models presented include induced point-dipoles, classical Drude oscillators, and fluctuating charge methods. The theoretical background of each method is followed by an introduction to extended Lagrangian integrators required for computationally tractable molecular dynamics simulations using polarizable force fields. The remainder of the review focuses on application studies using these methods. Emphasis is placed on water models, for which numerous examples exist, with a more thorough discussion presented on the recently published models associated with the Drude-based CHARMM and the AMOEBA force fields. The utility of polarizable models for the study of ion solvation is then presented followed by an overview of studies of small molecules (e.g., CCl 4 , alkanes, etc.) and macromolecule (proteins, nucleic acids and lipid bilayers) application studies. The review is written with the goal of providing a general overview of the current status of the field and to facilitate future application and developments.
Current methodologies for modelling electronic polarization effects in empirical force fields are presented. Emphasis is placed on the mathematical details of the methods used to introduce polarizability, namely induced dipoles, Drude oscillators or fluctuating charge. Overviews are presented on approaches used to damp short range electrostatic interactions and on Extended Langrangian methods used to perform Molecular Dynamics simulations. The final section introduces the polarizable methods under development in the context of the program CHARMM
Correlated calculations of molecular dynamic polarizabilities
The Journal of Chemical Physics, 1997
Frequency-dependent molecular polarizabilities of several molecules N 2 , CO, CO 2 , Cl 2 , C 2 H 2 , COS, and CS 2 are calculated by the equation-of-motion coupled cluster singles and doubles ͑EOM-CCSD͒ method. The EOM-CCSD CI-like, linear and quadratic methods for dynamic second-order properties are presented. The importance of electron correlation, the quadratic contribution, and orbital relaxation effects are assessed. London dispersion coefficients are calculated by numerical integration of the EOM-CCSD polarizabilities.
The Journal of Physical Chemistry A, 2015
In order to carry out a detailed analysis of the molecular static polarizability, which is the response of the molecule to a uniform external electric field, the molecular polarizability was computed using the finite-difference method for 21 small molecules, using density functional theory. Within nine charge population schemes (Löwdin, Mulliken, Becke, Hirshfeld, CM5, Hirshfeld-I, NPA, CHELPG, MK-ESP) in common use, the charge fluctuation contribution is found to dominate the molecular polarizability, with its ratio ranging from 59.9% with the Hirshfeld or CM5 scheme to 96.2% with the Mulliken scheme. The Hirshfeld-I scheme is also used to compute the other contribution to the molecular polarizability coming from the induced atomic dipoles, and the atomic polarizabilities in eight small molecules and water pentamer are found to be highly anisotropic for most atoms. Overall, the results suggest that (a) more emphasis probably should be placed on the charge fluctuation terms in futur...
Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations
Journal of Chemical Theory and Computation, 2007
The main thrust of this investigation is the development of models of distributed atomic polarizabilities for the treatment of induction effects in molecular mechanics simulations. The models are obtained within the framework of the induced dipole theory by fitting the induction energies computed via a fast but accurate MP2/Sadlej-adjusted perturbational approach in a grid of points surrounding the molecule. Particular care is paid in the examination of the atomic quantities obtained from models of implicitly and explicitly interacting polarizabilities. Appropriateness and accuracy of the distributed models are assessed by comparing the molecular polarizabilities recovered from the models and those obtained experimentally and from MP2/Sadlej calculations. The behavior of the models is further explored by computing the polarization energy for aromatic compounds in the context of cation-π interactions and for selected neutral compounds in a TIP3P aqueous environment. The present results suggest that the computational strategy described here constitutes a very effective tool for the development of distributed models of atomic polarizabilities and can be used in the generation of new polarizable force fields.
The Journal of Chemical Physics, 2003
The hybrid molecular-continuum model for polar solvation considered in this paper combines the dielectric continuum approximation for treating fast electronic ͑inertialess͒ polarization effects and a molecular dynamics ͑MD͒ simulation for the slow ͑inertial͒ polarization component, including orientational and translational solvent modes. The inertial polarization is generated by average charge distributions of solvent particles, composed of permanent and induced ͑electronic͒ components. MD simulations are performed in a manner consistent with the choice of solvent and solute charges such that all electrostatic interactions are scaled by the factor 1/ ϱ , where ϱ is the optical dielectric permittivity. This approach yields an ensemble of equilibrium solvent configurations adjusted to the electric field created by a charged or strongly polar solute. The electrostatic solvent response field is found as the solution of the Poisson equation including both solute and explicit solvent charges, with accurate account of electrostatic boundary conditions at the surfaces separating spatial regions with different dielectric permittivities. Both equilibrium and nonequilibrium solvation effects can be studied by means of this model, and their inertial and inertialess contributions are naturally separated. The methodology for computation of charge transfer reorganization energies is developed and applied to a model two-site dipolar system in the SPC water solvent. Three types of charge transfer reactions are considered. The standard linear-response approach yields high accuracy for each particular reaction, but proves to be significantly in error when reorganization energies of different reactions were compared. This result has a purely molecular origin and is absent within a conventional continuum solvent model.
Journal of Chemical Theory and Computation
We develop an extension of the time-dependent equation-ofmotion formulation of the polarizable continuum model (EOM-TDPCM) to introduce nonequilibrium cavity field effects in quantum mechanical calculations of solvated molecules subject to time-dependent electric fields. This method has been implemented in Octopus, a state-of-the-art code for real-space, real-time time-dependent density functional theory (RT-TDDFT) calculations. To show the potential of our methodology, we perform EOM-TDPCM/RT-TDDFT calculations of trans-azobenzene in water and in other model solvents with shorter relaxation times. Our results for the optical absorption spectrum of trans-azobenzene show (i) that cavity field effects have a clear impact in the overall spectral shape and (ii) that an accurate description of the solute shape (as the one provided within PCM) is key to correctly account for cavity field effects.
A simple treatment for incorporating induced polarization in computer simulations is formulated on the basis of the classical Drude oscillator model. In this model, electronic induction is represented by the displacement of a charge-carrying massless particle attached to a polarizable atom under the influence of the local electric field. The traditional self-consistent field ͑SCF͒ regime of induced polarization is reproduced if these auxiliary particles are allowed to relax instantaneously to their local energy minima for any given fixed configuration of the atoms in the system. In practice, such treatment is computationally prohibitive for generating molecular dynamics trajectories because the electric field must be recalculated several times iteratively to satisfy the SCF condition, and it is important to seek a more efficient way to simulate the classical Drude oscillator model. It is demonstrated that a close approximation to the SCF regime can be simulated efficiently by considering the dynamics of an extended Lagrangian in which a small mass is attributed to the auxiliary particles, and the amplitude of their oscillations away from the local energy minimum is controlled with a low-temperature thermostat. A simulation algorithm in this modified two-temperature isobaric-isothermal ensemble is developed. The algorithm is tested and illustrated using a rigid three-site water model with one additional Drude particle attached to the oxygen which is closely related to the polarizable SPC model of Ahlström et al. ͓Mol. Phys. 68, 563 ͑1989͔͒. The tests with the extended Lagrangian show that stable and accurate molecular dynamics trajectories for large integration time steps ͑1 or 2 fs͒ can be generated and that liquid properties equivalent to SCF molecular dynamics can be reproduced at a fraction of the computational cost.