TIP3P water 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. 

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

Simulations were performed with the NAMD simulation package (version 2.6) [83] using the all-atom Cornell et al. force field (parm99) [84], generated with the AMBER 10 package [85-87] and TIP3P water model [88]. Periodic boundary... 

In both the Charmm19 and Charmm22 force-fields, the basis was chosen to be a modified version of the TIP3P water model, since this model provides a satisfactory description of first-shell hydration and the energetics of liquid water while remaining... 

The experimental and computational study of bacterial thioredoxin, an E. coli protein, at THz frequencies is presented. The absorption spectrum of the entire protein in water was studied numerically in the terahertz range (0.1 - 2 THz). In our work, the initial X-ray molecular structure of thioredoxin was optimized using the molecular dynamical (MD) simulations at room temperature and atmospheric pressure. The effect of a liquid content of a bacterial cell was taken into account explicitly via the simulation of water molecules using the TIP3P water model. Using atomic trajectories from the room-temperature MD simulations, thioredoxin s THz vibrational spectrum and the absorption coefficient were calculated in a quasi harmonic approximation. 

Solvate the protein complex. Since minimizing an unhydrated protein can lead to significant unrealistic structural changes, it is very important to solvate the protein-ligand complex by means of an explicit solvent (SPCAE or TIP3P) water model (see later section Computational Details for Complex). 

Using the hybrid ADMP/ONIOM technique, Rega et al. [104] have published the result of a molecular dynamics simulation at the B3LYP/6-31+G(d,p) level and with AMBER/TIP3P water model of a chloride anion embedded in a cluster of 256 water molecules. The time step was 0.25 fs and they have performed a 3 ps simulation after thermalization, allowing them to report the atom-atom radial distribution functions. 

Note that a correct comparison of the absolute values of the temperatures of the percolation transitions of water in the hydration shells of ELP and Snase, obtained in simulations, with the real temperature scale needs special consideration, as the phase diagrams of the available water models differ noticeably from the phase diagram of real water (see [5, 6] for a comparative analysis of the phase diagrams of various water models). There are two main characteristic temperatures that can be used for estimating the temperature shift of the phase diagram of model water with the behavior of real water the critical temperature of the hquid-vapor phase transition and the temperature of the liquid density maximum. The latter temperature is the most important parameter for studies carried on close to ambient conditions. For example, the phase diagram of TIP3P water model is shifted downward by at least 35 K with respect to real water. 

The molecular simulations were performed according to the computational protocol illustrated in Fig. 26.2. In order to And the possible stable conformers of the monomers and the dimer, exhaustive conformational analysis with simultaneous variation of all torsion angles between non-hydrogen atoms was carried out employing a version of the OPLS force field [13] with modified ether group parameters [14]. The conformational search was performed both in vacuum and in explicit aqueous medium using the TIP3P water model [15]. The accumulated... 

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