TIP3P potential

Figure 5-2. Plot of CsOsCiOi angle of non-reducing saccharide residue 4-0-a -D-xylopyranosyl-a -D-xylopyranose from QM/MM molecular dynamics simulations using (a) a PM3/TIP3P potential and (b) a PM3CARB-1/TIP3P potential. Reproduced with permission from reference [66]. Copyright Elsevier 2004...

Equilibrium protein water shell obtained by minimizing of the system in chosen TIP3P potential can be stndied from the point of accordance of its topological model to th-cycles model. We consider its geometrical and topological characteristics statistically and with the help of concrete examples. 

Table 2 Computed Relative Free Energies of Hydration (kcal/mol) for Selected Organic Compounds Using the Combined AM1/TIP3P Potential ...

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... 

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. 

TIP3P Transferable intermolecular potential with three points... 

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