TIP3P model

Often yon need to add solvent molecules to a solute before running a molecular dynamics simiilatmn (see also Solvation and Periodic Boundary Conditions" on page 62). In HyperChem, choose Periodic Box on the Setup m en ii to enclose a soln te in a periodic box filled appropriately with TIP3P models of water inole-cii les. 

Hg. 6.13 Minimum energy structure for water dimer with TIP3P model... 

From the starting structures (PDB file), the full complement of hydrogens is added using a utility within CHARMM. The entire protein is then solvated within a sphere of TIP3P model waters, with radius such that all parts of the protein were solvated to a depth of at least 5 A. A quartic confining potential localized on the surface of the spherical droplet prevented evaporation of any of the waters during the course of the trajectory. The fully solvated protein structure is energy minimized and equilibrated before the production simulation. 

With increasing use of such models, methods are likely to become more concisely defined in the near future. At present, the models for which protocols and parameters have been most clearly defined and where a fair number of applications have appeared applying those models in a consistent fashion include the aheady noted AM1/TIP3P model (more generally AMl/OPLS when solvents other than water are employed in the MM region) and a similarly fashioned HF/3-21G/OPLS model (Freindorf and Gao 1996). Implementations carrying the QM level as far as coupled-cluster theory have been reported (Kongsted et al. 2003). 

In Table 2 we summarize some of their findings. The table shows the amount of water in the ionic liquid, the amount of ionic liquid in the water, and the width of the interface separating the two phases at the end of the simulation for the different force fields. It is seen that the popular TIP3P model gives quite different results from those of the other force fields and in the simulation of the mixing process there is not even a well defined interface. The other two force fields give similar results. All simulations support that the ionic liquid is essentially water-free, as should be. 

In ab initio QM/MM approaches, the Coulomb interaction is calculated accurately. Therefore, in these implementations, only the Lennard-Jones parameters on the QM atoms are reparameterized. Freindorf and Gao [47] obtained the Lennard-Jones parameters by fitting the combined QM/MM results to the full ab initio HF/6-31G(d) results. They chose over 80 hydrogen-bonded complexes of organic compounds with water molecules. In the combined QM/MM calculation, the QM molecule was calculated by using ab initio HF/3-21G, while for the MM water molecules, the TIP3P model [48] was used. It is not clear whether these parameters (obtained from calculations of molecular complexes) are really suitable to be used in the condensed phase simulation or not. 

A seven residue substrate model was chosen on the basis of its similarity to an inhibitor that was crystallized in a complex with HIV-1 PR. It includes the Tyr-Pro cleavage site which is common to a few sites of the gag fusion protein, the substrate of HIV-1 PR. This model was constructed from the inhibitor by "mutating" only two of the inhibitor s residues. MD simulations were carried out with CHARMM (Brooks et al., 1982) and water molecules were represented by a modified (Steinbach and Brooks, 1993) TIP3P model (Jorgensen et al., 1983). Five hundred water molecules were employed (minimal solvation). 

If one calculates the sensitivity coefficients of different properties of an aqueous system with respect to the atomic partial charges of the water models, the sensitivity coefficients obtained from an effective charge model can be different from those of a polarizable model. This difference was found in calculations of the charge sensitivities of different properties of liquid water with two effective charge models (the SPC and the TIP3P models ) and a polarizable water model > (Table 1), although the differences were more pronounced for sensitivity coefficients of some types than for others. Therefore, in using sensitivity coefficients to help identify the determinants of bio(molecular) proper-... 

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