TIP3P/TIP4P models

The explicit water models most currently used are TIP3P, TIP4P 202, TIP5P203, SPC and SPC/E.204 The parameters in all models are empirically adjusted so that they reproduce the enthalpy of vaporization and the density of water.129 TIP3P is probably the most commonly used model. However, when selecting a water... 

Figure 1 Structural features of the TIP3P, TIP4P and TIP5P water models 2 COMPUTATIONAL METHODS...

The setup of a simulation system, which includes a protein embedded into a lipid bilayer requires additional efforts in comparison to a system with a soluble protein. There are different choices the researcher has to make regarding to the nature of the phospholipid bilayer used, the temperature at which the simulations should be performed (this also depends on the nature of the bilayer), the force field, the water model (e.g. SPC, SPC/E, TIP3P, TIP4P, TIP5P this also depends on the choice of the force field), and many more. 

Some properties of liquid water computed with the TIP3P and TIP4P models are compared with experimental data in... 

A complete set of intermolecular potential functions has been developed for use in computer simulations of proteins in their native environment. Parameters have been reported for 25 peptide residues as well as the common neutral and charged terminal groups. The potential functions have the simple Coulomb plus Lennard-Jones form and are compatible with the widely used models for water, TIP4P, TIP3P and SPC. The parameters were obtained and tested primarily in conjunction with Monte Carlo statistical mechanics simulations of 36 pure organic liquids and numerous aqueous solutions of organic ions representative of subunits in the side chains and backbones of proteins... 

Table 17.7 Force field parameters for the developed C02(TIP3P), C02(TIP4P), and C02(TIP4P-Ew) carbon dioxide models ...

Fig. 17.7 The calculated solubility of C02 in water at 1 atm using the Steele [24] C02 [down triangle, green] model with TIP3P water, the developed C02(TIP3P) [up triangle, blue], C02(TIP4P) [circle, red], C02(TIP4P-Ew)[left pointing triangle, pink] models with their respective water models, compared against the experimental values [square, black] [25, 26]...

It is often very helpful to apply MD simulations prior to a conformational search in order to gather information about the important H-bonded species in solution [133-136]. In our studies we used the Sander module in the AMBER9 suite of programs [137], the AMBER ff99 force field based on molecular mechanics, and the TIP3P [138] or TIP4P [139] water model in the simulations. The ratio between... 

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