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| TIP3P | |
|---|---|
| Name | TIP3P |
| Developer | Harvard University; Martin Karplus group; William L. Jorgensen |
| Released | 1983 |
| Latest release | 1980s–1990s parameter sets |
| Programming language | force field parameter files |
| License | academic use |
TIP3P.
TIP3P is a three-site rigid classical water model widely used in biomolecular simulations and computational chemistry. It was introduced to reproduce experimental properties of liquid water while remaining computationally inexpensive for use with force fields developed at Yale University and in the Harvard and Columbia University communities. The model played a formative role in the development of biomolecular simulation protocols at institutions such as Brookhaven National Laboratory, Argonne National Laboratory, Lawrence Livermore National Laboratory, and in research groups led by Martin Karplus, Michael Levitt, and Arieh Warshel.
TIP3P represents the water molecule with three interaction sites corresponding to atomic centers on oxygen and two hydrogens, employing fixed bond lengths and angles derived from gas-phase geometries. Lennard–Jones parameters are assigned to the oxygen site to model dispersion and repulsion, while partial charges on oxygen and hydrogens produce the permanent dipole; these parameters were tuned relative to experimental observables measured at facilities such as National Institute of Standards and Technology and techniques developed by researchers at University of Minnesota. Electrostatic interactions are usually treated with Ewald summation methods implemented in software packages from University of California, San Diego and University of Illinois at Urbana-Champaign, and long-range corrections are commonly applied as in codes maintained by teams at University of Cambridge and University of California, Berkeley.
The original formulation was developed by researchers associated with Yale University and introduced alongside other models such as SPC and ST2 by groups at Brookhaven National Laboratory and Argonne National Laboratory. Subsequent adaptations include a version optimized for use with Ewald methods, a modified-charge variant for compatibility with polarizable force fields developed at University of Oxford and University of Michigan, and reparameterizations introduced by teams at California Institute of Technology and Massachusetts Institute of Technology. Variants have emerged from collaborations involving researchers at Max Planck Society, CNRS, and RIKEN, and have been incorporated into major molecular dynamics packages maintained by groups at DE Shaw Research, Schrödinger, AMBER, and GROMACS projects.
TIP3P has been employed extensively in simulations of proteins studied by groups at Stanford University, University of Cambridge, and University of Oxford, nucleic acids investigated at Cold Spring Harbor Laboratory and European Molecular Biology Laboratory, lipid bilayers modeled by teams at Scripps Research Institute and University of California, San Diego, and small-molecule solvation studied by researchers at Imperial College London. It is routinely used in free energy calculations performed by laboratories at University of California, Berkeley and Princeton University, in folding studies associated with University of Washington and University of Illinois at Urbana-Champaign, and in membrane transport simulations linked to Johns Hopkins University and University of Toronto collaborations. Its low computational overhead has made it a choice for long-timescale simulations enabled by resources such as those at Oak Ridge National Laboratory and National Center for Supercomputing Applications.
TIP3P reproduces some bulk properties of liquid water, such as density at ambient conditions measured by National Metrology Institutes and dielectric behavior matching data from experiments at Max Planck Institutes, but it exhibits notable deviations for diffusion coefficients, surface tension, and temperature-dependent density anomalies characterized in studies at Lawrence Berkeley National Laboratory and Pacific Northwest National Laboratory. The absence of explicit polarizability limits its accuracy for systems where induction effects are significant, a limitation highlighted in comparisons with polarizable models developed at University of California, Santa Barbara and University of Minnesota. Additionally, the rigid geometry and fixed partial charges can lead to systematic errors in hydrogen-bond kinetics reported by groups at Weizmann Institute of Science and École Polytechnique.
Compared with other three-site models such as SPC and three-point reparameterizations by groups at University of Potsdam and ETH Zurich, TIP3P often offers faster convergence in biomolecular contexts but at some cost to fidelity in thermodynamic quantities. Four-site and five-site models like TIP4P and TIP5P developed by researchers at University of Leeds and University of Barcelona introduce off-atom charge sites to better match experimental phase behavior measured by International Union of Crystallography-associated studies, while polarizable models from University of Illinois and University of Houston address inducible dipoles for improved spectroscopy predictions. Large-scale benchmarks performed by consortia including PDB-associated groups, Bioinformatics Institute teams, and industrial partners at Pfizer and Novartis continue to inform model choice depending on trade-offs between computational cost and agreement with observables curated by laboratories across Europe and the United States.
Category:Water models