Comparison of simple potential functions for simulating liquid water

By W. L. Jorgensen, J. Chandrasekhar, Jeffry D. Madura, R. Impey, M. Klein. 1983

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Citations in the corpus

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics (2016, methodology): “It loads a PDB file, models the forces with the AMBER99SB-ILDN force field [20] and TIP-3P water model [21], performs a local energy minimization to eliminate clashes, and then simulates 1 million steps of Verlet dynamics.”
Driven to Near-Experimental Accuracy by Refinement via Molecular Dynamics Simulations (2019, methodology): “The initial protein models were solvated with TIP3P water molecules 39 in a periodic rectangular box with at least 9 Å of solvent to the box edge.”
AlphaDesign: A de novo protein design framework based on AlphaFold (2021, methodology): “Each protein or protein complex was solvated using atomistic TIP3P water [92] with a minimum of 10 Å of padding to form a cubic periodic box and then electrically neutralized with an ionic concentration of 0 .”
Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials. (2016, methodology): “escribed in Section 5.1. Here we study benzene solvated by water. To describe the structure and interactions of the water molecules in the all-atom simulations we use the TIP3P three-site water model [138]. We consider two different systems of water-solvated benzene: a benzene dimer solvated by 874 ”
Multiscale simulation of soft matter: from scale bridging to adaptive resolution. (2008, background): “The single-site5 water model (75) reproduces remarkably well the essential thermodynamic and structural features of water, as obtained by detailed all-atom simulations using the rigid TIP3P (90) water model.”