TIP3P

The explicit definition of water molecules seems to be the best way to represent the bulk properties of the solvent correctly. If only a thin layer of explicitly defined solvent molecules is used (due to hmited computational resources), difficulties may rise to reproduce the bulk behavior of water, especially near the border with the vacuum. Even with the definition of a full solvent environment the results depend on the model used for this purpose. In the relative simple case of TIP3P and SPC, which are widely and successfully used, the atoms of the water molecule have fixed charges and fixed relative orientation. Even without internal motions and the charge polarization ability, TIP3P reproduces the bulk properties of water quite well. For a further discussion of other available solvent models, readers are referred to Chapter VII, Section 1.3.2 of the Handbook. Unfortunately, the more sophisticated the water models are (to reproduce the physical properties and thermodynamics of this outstanding solvent correctly), the more impractical they are for being used within molecular dynamics simulations. 

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. 

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. 

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

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. 

Proper condensed phase simulations require that the non-bond interactions between different portions of the system under study be properly balanced. In biomolecular simulations this balance must occur between the solvent-solvent (e.g., water-water), solvent-solute (e.g., water-protein), and solute-solute (e.g., protein intramolecular) interactions [18,21]. Having such a balance is essential for proper partitioning of molecules or parts of molecules in different environments. For example, if the solvent-solute interaction of a glutamine side chain were overestimated, there would be a tendency for the side chain to move into and interact with the solvent. The first step in obtaining this balance is the treatment of the solvent-solvent interactions. The majority of biomolecular simulations are performed using the TIP3P [81] and SPC/E [82] water models. 

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... 

In all cases the calculations were performed using QM/MM methodology that includes the pseudobond model for the QM/MM boundary [13,39,41]. This methodology has been implemented in a modified version of Gaussian 98 [42], which interfaces to a modified version of TINKER [43], The AMBER94 all-atom force field parameter set [44] and the TIP3P [45] model for water were used. 

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...

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...

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. 

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... 

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