Simple point charge extended water model

The extended simple point charge (SPC/E) model [59] is used. This model is known to give reasonably accurate values of static dielectric permittivity of liquid water at ambient conditions [60]. The MD simulations were performed for both H2O and D2O with the system size of 1024 particles at 220 K, 240 K, 267 K, 273 K, 300 K, and 355 K. The parallel molecular dynamics code for arbitrary molecular mixtures (DynaMix) is implemented by Lyubartsev and Laaksonen [61]. The simulations have been carried out on a Linux cluster built on the Tyan/Opteron 64 platform, which enables calculations of relatively long trajectories for a system of 1024 water molecules. The simulation run lengths depend on temperature and are in the range between 1 ns and 4 ns for the warmest and coldest simulation, respectively. As the initial condition was a cubic lattice, the equilibration time was chosen to be temperature dependent in the range from 200 ps at 355 Ktol ns at 200K. 

Let us consider Met-enkephalin (Tyr-Gly-Gly-Phe-Met) with 75 atomic sites in three different solvents including water. The model of a wee ter molecule is the extended simple point charge (SPG/E) model [19]. It is assumed that the peptide is immersed in the solvent at infinite dilution. The potential-energy functions and parameters are adopted from KONF90 [20] that is based on ECEPP/2 [21]. The peptide and solvent molecules comprise the interaction sites (atoms). The interaction between the peptide molecule and a water molecule is expressed as the sum of the site-site pair interactions that have the form... 

SPC/E simple point charged/extended model (for water)... 

Solvent. The water molecules conformed to the Simple Point (Jbarge Extended model (SPC/E) (4), which is summarized in Table I. The non-polar" solvents were taken as monoatomic non-charged atomic liquids with the same Lennard-Jones (6-12) parameters as oxygen in water, making an argon-like solvent. 

Atomistic MD models can be extended to the coarse-grained level introduced in the previous section, which is determined by the dimension of the backbone chain and branch. For the precise description of water molecular behavior, simple point charge (SPC) model was adopted (Krishnan et al., 2001), which can be used to simulate complex composition systems and quantitatively express vibrational spectra of water molecules in vapor, liquid, and solid states. The six-parameter (Doh, o , fi, Lye, Lyy, and Lee) SPC potential used for the water molecules is shown in Equation (24) ... 

The Effects of Pressure on Structural and Dynamical Properties of Associated Liquids Molecular Dynamics Calculations for the Extended Simple Point Charge Model of Water. 

P.E. Smith and W.F. van Gunsteren, Consistent dielectric properties of the simple point charge and extended point charge water models at 277 and 300 K, J. Chem. Phys., 100 (1994) 3169-3174. 

K. Bagchi, S. Balasubramanian, and M. L. Klein,/. Chem. Phys., 107, 8561 (1997). The Effects of Pressure on Structural and Dynamical Properties of Associated Liquids Molecular Dynamics Calculations for the Extended Simple Point Charge Model of Water. 

Hummer G, Grdnbech-Jensen N, Neumann M. Pressure calculation in polar and charged systems using Ewald summation results for the extended simple point charge model of water. J. Chem. Phys. 1998 109 2791. 

Model Channel Ion Currents in NaCl-Extended Simple Point Charge Water Solution with Applied-Field Molecular Dynamics. 

The Na-AOT reverse micelle is a widely investigated reverse micelle system made up of the sodium salt of a two-tailed anionic surfactant, sodium di(2-ethylhexyl) sulfosuccinate. The interior of the aqueous reverse micelle is modeled as a rigid cavity, with a united atom representation for the sulfonate head group (Faeder and Ladanyi 2000 Pal et al. 2005). The head groups protrude from the cavity boundary and are tethered only in the radial direction by means of a harmonic potential. Interactions between reverse micelles are neglected in the model hence periodic boundary conditions and Ewald summations for the electrostatics are not required. Water is treated using the extended simple point charge, or SPC/E, model and the potential parameters for all the species are listed in Table 6.1. 

Chandra (Chandra, 2000) investigated the specific role of ions on H-bonds between water molecules using molecular dynamics. The systems chosen were NaCl and KCl in water at various concentrations (from OM to 3.35M). Water molecules were modeled by the extended simple point charge (SPC/E) potential and ions were modeled as charged Lennard-Jones particles. For analyzing the hydrogen bond breaking dynamics, the author calculated the time correlation functions Shb(0 and S HB(f). Shb(0 describes the probability that an initially... 

The parameters of five representative and commonly used water models in MD simulations are listed in Table 52.1. SPC is the short term for simple point charge, and SPC/E denotes the extended simple point charge model with charges on the oxygen and hydrogen modified to improve the classical SPC water model, the SPC/E model results in a better density and diffusion constant than the SPC model. TIP in TlPnP stands for transferable intermolecular potential, while nP means there are n points used in the corresponding water model. 

This theory, when applied to the SPC water geometry but with a fixed dipole equal to that of an isolated H2O molecule, p = 1.85D, leads to the result = 2.62D. This is in good agreement with the well-known extended simple point charged model SPC/E which allows for the polarisation correction. This validates the self-consistent mean-field procedure. As an illustration of the anion polarisation effect. Fig. 7... 

When simulations are applied to studies on the surfaces and interfaces of ice near T, it is important to select a potential model of H2O that is suitable for simulations of both ice and water near To date, many potential models of H2O have been proposed. Several of the models, such as the extended simple point charge model (SPC/E) [56], T1P4P [57], and TIP5P [58] models, have been used by many researchers, especially for simulations of liquid water. In these models, an H2O molecule is represented as an electrically neutral, simple rigid molecule (Figure 17.11). Commonly in aU of the models, a positive charge is placed on each hydrogen (H) atom. 

The model was originally proposed by Paul Drude in 1902 as a simple way to describe dispersive properties of materials [108]. A quantum version of the model (including the zero-point vibrations of the oscillator) has been used in early applications to describe the dipole-dipole dispersion interactions [109-112]. A semiclassical version of the model was used more recently to describe molecular interactions [113], and electron binding [114]. The classical version has been subsequently used for ionic crystals [115-120], simple liquids [121-127], water [128-135], and ions [136-139], and in recent decades has seen widespread use in MD and MC simulations. In recent years, the Drude model was extended to interface with QM approaches in QM/MM methods [140], facilitated by the simplicity of the model in that it only includes additional charge centers. 

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