Ilario G. Tironi

A generalized reaction field method for molecular dynamics simulations

Molecular dynamics simulations of ionic systems require the inclusion of long‐range electrostatic forces. We propose an expression for the long‐range electrostatic forces based on an analytical solution of the Poisson–Boltzmann equation outside a spherical cutoff, which can easily be implemented in molecular simulation programs. An analytical solution of the linearized Poisson–Boltzmann (PB) equation valid in a spherical region is obtained. From this general solution special expressions are derived for evaluating the electrostatic potential and its derivative at the origin of the sphere. These expressions have been implemented for molecular dynamics (MD) simulations, such that the surface of the cutoff sphere around a charged particle is identified with the spherical boundary of the Poisson–Boltzmann problem. The analytical solution of the Poisson–Boltzmann equation is valid for the cutoff sphere and can be used for calculating the reaction field forces on the central charge, assuming a uniform continuum ...

LATTICE-SUM METHODS FOR CALCULATING ELECTROSTATIC INTERACTIONS IN MOLECULAR SIMULATIONS

When simulating a periodic molecular system, lattice sum methods may be used to evaluate the electrostatic interactions without resorting to an unphysical truncation of the potential. In a previous publication, we compared the computational efficiency of the Ewald and Particle‐Particle Particle‐Mesh (PPPM) lattice‐sum methods. Because the PPPM method discretizes the field equations and utilizes the highly efficient fast Fourier transform algorithm, it requires significantly less computational effort than the Ewald method and scales almost linearly with system size. In this paper, we take a more detailed look into the theory behind the lattice‐sum methods to clarify the underlying similarities between the Ewald method and the PPPM method. We also investigate the errors introduced by different approximation used in the discretization of the field equations in the PPPM method.

A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular Systems

Abstract We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods for calculating electrostatic interactions in periodic molecular systems. A brief comparison of the theories shows that the methods are very similar differing mainly in the technique which is used to perform the “k-space” or mesh calculation. Because the PPPM utilizes the highly efficient numerical Fast Fourier Transform (FFT) method it requires significantly less computational effort than the Ewald method and scales almost linearly with system size.

A molecular dynamics simulation study of chloroform

Three different chloroform models have been investigated using molecular dynamics computer simulation. The thermodynamic, structural and dynamic properties of the various models were investigated in detail. In particular, the potential energies, diffusion coefficients and rotational correlation times obtained for each model are compared with experiment. It is found that the theory of rotational Brownian motion fails in describing the rotational diffusion of chloroform. The force field of Dietz and Heinzinger was found to give good overall agreement with experiment. An extended investigation of this chloroform model has been performed. Values are reported for the isothermal compressibility, the thermal expansion coefficient and the constant volume heat capacity. The values agree well with experiment. The static and frequency dependent dielectric permittivity were computed from a 1·2 ns simulation conducted under reaction field boundary conditions. Considering the fact that the model is rigid with fixed par...

On the relative merits of flexible versus rigid models for use in computer simulations of molecular liquids

Abstract The relative merits of the use of flexible versus rigid models in molecular dynamics simulations of simple molecular liquids are discussed and compared using liquid water as an example. It is concluded that the introduction of flexibility creates more problems than it solves, and does not improve the accuracy of rigid simple point charge models.

Computer simulation of protein motion

The application of molecular dynamics computer simulation methods to study the dynamics of proteins is reviewed with an eye to its possibilities and limitations. Examples are given, mainly using nanosecond trajectories of the proteins bovine pancreatic trypsin inhibitor and lysozyme, of the different protein properties, of which the dynamics can be or cannot be sampled on a nanosecond time scale. It is concluded that the major asset of the simulation technique is that the different factors contributing to the dynamics of a particular process can be analyzed at atomic detail, as long as one has sampled the appropriate time scale.

A Molecular Dynamics Simulation Study of Liquid Carbon Tetrachloride

Abstract We present an all-atom force field model for liquid carbon tetrachloride for use in molecular dynamics simulations. The model is rigid with tetrahedral symmetry and the molecular interactions are represented in terms of site-site Lennard-Jones potential energy functions. With the molecular dynamics method we are able to accurately predict physical quantities of CCl4 including shear viscosity, the excess Helmholtz energy and the surface tension.

Space-time correlated reaction field: A stochastic dynamical approach to the dielectric continuum

In molecular dynamics (MD) simulations, the continuum description of electrostatic interactions has been based in most cases on the static response of the dielectric continuum. In this work, a time-dependent reaction field expression including stochastic and friction terms is derived in analogy to the generalized Langevin equation involving hydrodynamic interactions. Simulations of water using the extended simple-point charge model have been performed under different boundary conditions. The effects of a time-dependent treatment of the reaction field are demonstrated by comparing the results to those of MD simulations using a static, instantaneous reaction field and of MD simulations employing the Ewald sum. It is shown for the first time that the straight cutoff approach not only leads to a disruption of the time, but also of the spatial correlation of the dipole moment.