SPC water model

Figure 2 Pair correlation functions of 0-0 and O-H at ( puted with the parameters of the SPC water model.

Fig. 9.5. Plot of ln[ 2Q.(s)/ 0)(e)]. The region between —2.5kcalmol 1 and - 0.5 kcal moP1 is satisfactorily linear, and (9.17) yields T w 302 K, in good agreement with the simulation temperature of 298 K. The intercept gives //ex =2.5 kcal mol-1 in agreement with a value of 2.5 kcalmoP1 for the SPC water model [63]...

Liquid water is an important medium in which most biomolecules perform their function. Pure liquid water may seem like a very simple system, where one may be able to identify the determining factors of its properties easily, but this is not always found to be the case. Table 2 gives examples of studying several thermodynamic properties of liquid water using a flexible SPC water model in a molecular dynamics simulation. This flexible water model was characterized by the following interaction potential ... 

Table 2. The Most Significant Parameters of the Flexible SPC Water Model That Control Different Thermodynamic Properties of Liquid Water ... 

MD simulations for the SPC water model. Interpolated from (Mizan et al. 1994). 

Figure 18. Spectral densities (in aibitraiy units) of low-fiequency translational motions for supercritical water at liquid-like densities. The spectra of liquid water under ambient conditions for the BJH (Jancso et al. 1984) and SPC water models are given for comparisoa...

Lockwood and colleagues performed an analysis of decoherence in a ruthenium-modified blue copper protein similar to amicyanin. They found a short characteristic decoherence time of 2.4 fs, which they attributed on one hand to the diverging motion of the protein nuclei and on the other hand to the solvent molecules. Their conclusion was that both solvent and protein dynamics can affect both the rate and mechanism of electron transfer which is different to our conclusions on solvated TTQ where the solvent does not seem to play any role in decoherence. More precisely, solvent molecules start to play a role once decoherence has already occurred due to the intramolecular motions within the TTQ. Lockwood et al. used a classical force field for all the atoms, including those of the copper and ruthenium complexes, and a rigid SPC water model. In addition they did not carry out large ensembles of diverging... 

The 3 point TIP3P and SPC water models, usually treated as rigid molecules but in some cases allowed to be flexible, were used in all simulations. With the many charges along the DNA phosphate backbone there is an issue about the ionic conditions, and one finds three different approaches here (Table 1) ... 

All three non-polarizable models are described as effective rigid pair potentials composed of Lennard-Jones (U) and Coulombic terms, differing only on the size of the Coulombic charge. The SPC water model is given by, ... 

SPC water model, namely (a) the exceptional overall performance of the SPC model considering its non-polarizable nature (b) the precarious description of the near-critical behavior of water, in particular, the inaccurate prediction of the critical conditions and (c) the role played by the fortuitous compensation of factors such as in the product e-T = s(T/Tc, p/Pc) T involved in the reference for the mean-force potential WAc(ro). ... 

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. 

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