Molecular dynamics simulation for liquid water using a polarizable and flexible potential

Abstract

A molecular dynamics simulation for liquid water at room temperature is reported. A sample of 1000 water molecules has been analyzed with the Nieser-Corongiu-Clementi polarizable potential, to which is added vibrational flexibility. The sample was contained in a cubic box subject to periodic boundary conditions, a cutoff radius of 15.54 8, was used in evaluating energies and forces, the long-range interactions were taken into account with the reaction field method, and the integration of the equation of motion has been performed using a sixth-order Gear predictorcorrector algorithm. The simulation, after 35 ps of equilibration time, has been carried out for 10.4 ps with a time step of 1.25 x s. The trajectories and velocities, collected in the production phase of the simulation, have been used to compute the geometry of the water molecule within the liquid, thermodynamical quantities, the pair correlation functions, the Dore neutron pair correlation function, X-ray and neutron scattering structure functions, translational, rotational, orientational autocorrelation functions and their Fourier transforms, mean square displacements, diffusion coefficients, and N M R relaxation times. A detailed study on the spectral density is presented, and good agreement is found with the most recent infrared, Raman, and neutron scattering laboratory data. All the simulated properties so far analyzed are in good agreement with experimental data, and, with confidence, we can assess that our ab initio polarizable potential with inclusion of vibrations is the most reliable water potential in today's literature for the description of water.

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications

“…To meet the need of a computationally tractable yet appropriately accurate model of water an extremely large number of polarizable potentials for water have been developed. These include models based on induced point dipoles [140,149-167], Drude oscillators [72,74-77], fluctuating charge models [15,25,91,101,115,148,168,169] and hybrid induced dipole/fluctuating charge methods [35]. The reader is referred to a previous review on a number of additive and polarizable water models for additional information [16].…”

Analysis of anisotropic local field in sum frequency generation spectroscopy with the charge response kernel water model

“…31,32 On the other hand, the MD calculation for this approach requires a sophisticated molecular model beyond the usual flexible and polarizable force field. [33][34][35][36][37][38][39][40][41] Calculation of instantaneous dipole and polarizability of the interface is a key ingredient of the MD simulation of this approach, as discussed below. For the time-dependent calculation of SFG spectra, we propose to use the charge response kernel ͑CRK͒ theory [42][43][44][45][46] as a general and promising modeling method.…”

A Self-Consistent Space-Domain Decomposition Method for QM/MM Computations of Protein Electrostatic Potentials

“…[67][68][69][70] Significant effort has been focused on the development of both polarizable protein force fields [6][7][8][9][10][11][12][13][14][15][67][68][69][70] and polariz-able models for small molecules. [15][16][17][18][19][20][21][22][23][24][25] While these methods are expected to become routine practice, no polarizable force field has so far been widely implemented for protein modeling. Parameters are still under development, and published applications are limited to those from the development groups.…”