TIP3P water

Use a constant dielectric of 1.0 with TIP3P water molecules m a periodic box. Because of ihe paramelerizatioii of TIP3P molecules, using a distart ce-dependen t dielectric or a value other th an 1.0 gives un Tialiiral results. 

HyperChem uses the TIP3P water model for solvation.You can place the solute in a box of TIP3P water molecules and impose periodic boundary conditions. You may then turn off the boundary conditions for specific geometry optimization or molecular dynamics calculations. However, this produces undesirable edge effects at the solvent-vacuum interface. 

Figure 7-3. Active site properties of CAII from SCC-DFTB/MM-GSBP simulations [91]. (a) The root mean square differences between the RMSFs calculated from GSBP simulations (WT-20 and WT-25 have an inner radius of 20 and 25 A respectively) and those from Ewald simulation, for atoms within a certain distance from the zinc, plotted as functions of distance from the zinc ion that die center of die sphere in GSBP simulations is the position of the zinc ion in the starting (crystal) structure, (b) The diffusion constant for TIP3P water molecules as a function of the distance from the zinc ion in different simulations...

Rao and Singh32 calculated relative solvation free energies for normal alkanes, tetra-alkylmethanes, amines and aromatic compounds using AMBER 3.1. Each system was solvated with 216 TIP3P water molecules. The atomic charges were uniformly scaled down by a factor of 0.87 to correct the overestimation of dipole moment by 6-31G basis set. During the perturbation runs, the periodic boundary conditions were applied only for solute-solvent and solvent-solvent interactions with a non-bonded interaction cutoff of 8.5 A. All solute-solute non-bonded interactions were included. Electrostatic decoupling was applied where electrostatic run was completed in 21 windows. Each window included 1 ps of equilibration and 1 ps of data... 

The As calculations (Equation (3.95)) were based on the Poisson equation, solved for a five-zone model (Section 3.5.4, Inhomogeneous Media) in which the solute (zone 1) was surrounded by four dielectric zones (2-5). A simplified schematic picture is given in Figure 3.26, but in the actual calculations, the zone boundaries were based on structures obtained from classical molecular dynamics (MD) simulations (with inclusion of a few thousand TIP3P water molecules and Na+ counterions to neutralize the negative charge from the DNA). Each zone was assigned optical and static dielectric constants (sxk and e0k, k = 1, 5). For the solute (zone 1), = e0k = 1.0 was adopted. For zones 2,3,... 

The literature force field models were used with the TIP3P water model to calculate the interaction of the CO2 with a single water molecule, as was done in the ab initio calculations presented above [22-24], When the literature CO2 complexes were compared to the ab initio complexes, the Steele model provided the best match with the ab initio data, with an interaction energy and distance of... 

As shown in Fig. 17.7, the CO2 models developed for aqueous simulations, show drastic improvement over the previous model(s). The CO2CITP3P) model shows improvement in the quantitative agreement with the experimental data, although the overall shape of the solubility curve is not obtained. This can most likely be explained by the ability of the TIP3P water model to accurately reproduce the experimental density curve over the temperature range in question for most... 

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]...

Fig. 18.1 Free energy vs. temperature for the liquid and solid phases using the TIP3P water model...

Fig. 7 Structure of imatinib (space-filling model) complex with c-Abl kinase (cartoon) from PDB (2HYY) after 500 ps of dynamics simulation in periodic box of TIP3P water. Figure prepared using Pymol...

Molecular dynamics simulation with 412 TIP3P water molecules. 

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