ArticleThe Journal of chemical physics2012
Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models.
Article in The Journal of chemical physics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed.
- Computationally Efficient Polarizable MD Simulations: A Simple Water Model for the Classical Drude Oscillator Polarizable Force Field.The journal of physical chemistry letters · 2025Article
- Revised 4-Point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ.Journal of chemical theory and computation · 2024Article
- Free Energy Density of a Fluid and Its Role in Solvation and Binding.Journal of chemical theory and computation · 2024Article
- Coarse-Graining Waters: Unveiling The Effective Hydrophilicity/Hydrophobicity of Individual Protein Atoms and The Roles of Waters' Hydrogens.Journal of chemical theory and computation · 2023Article
- Celastrol attenuates hepatitis C virus translation and inflammatory response in mice by suppressing heat shock protein 90β.Acta pharmacologica Sinica · 2023Article
- Exploration of the Product Specificity of chitosanase CsnMY002 and Mutants Using Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2023Article
- Interfacial interaction-driven rheological properties of quartz nanofluids from molecular dynamics simulations and density functional theory calculations.Journal of molecular modeling · 2022Article
- Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.Chemical reviews · 2019Review
- Multi-resolution dimer models in heat baths with short-range and long-range interactions.Interface focus · 2019Article
- Assimilating Radial Distribution Functions To Build Water Models with Improved Structural Properties.Journal of chemical information and modeling · 2018Article
- Determination of the μ-Conotoxin PIIIA Specificity Against Voltage-Gated Sodium Channels from Binding Energy Calculations.Marine drugs · 2018Article
- Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics.Proceedings. Mathematical, physical, and engineering sciences · 2016Article
- Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen-Hydrogen Correlations.Journal of chemical theory and computation · 2015Article
- From molecular dynamics to Brownian dynamics.Proceedings. Mathematical, physical, and engineering sciences · 2014Article
- Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimation.Journal of computational chemistry · 2014Article
- Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules.Journal of chemical information and modeling · 2013Article
- Assessing the accuracy of inhomogeneous fluid solvation theory in predicting hydration free energies of simple solutes.The journal of physical chemistry. B · 2013Article
- Matching of additive and polarizable force fields for multiscale condensed phase simulations.Journal of chemical theory and computation · 2013Article
- Benchmarking the thermodynamic analysis of water molecules around a model beta sheet.Journal of computational chemistry · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
Water is one of the simplest molecules in existence, but also one of the most important in biological and engineered systems. However, understanding the structure and dynamics of liquid water remains a major scientific challenge. Molecular dynamics simulations of liquid water were performed using the water models TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP to calculate the radial distribution functions (RDFs), the relative angular distributions, and the excess enthalpies, entropies, and free energies. In addition, lower-order approximations to the entropy were considered, identifying the fourth-order approximation as an excellent estimate of the full entropy. The second-order and third-order approximations are ~20% larger and smaller than the true entropy, respectively. All four models perform very well in predicting the radial distribution functions, with the TIP5P-Ewald model providing the best match to the experimental data. The models also perform well in predicting the excess entropy, enthalpy, and free energy of liquid water. The TIP4P-2005 and SWM4-NDP models are more accurate than the TIP3P-Ewald and TIP5P-Ewald models in this respect. However, the relative angular distribution functions of the four water models reveal notable differences. The TIP5P-Ewald model demonstrates an increased preference for water molecules to act both as tetrahedral hydrogen bond donors and acceptors, whereas the SWM4-NDP model demonstrates an increased preference for water molecules to act as planar hydrogen bond acceptors. These differences are not uncovered by analysis of the RDFs or the commonly employed tetrahedral order parameter. However, they are expected to be very important when considering water molecules around solutes and are thus a key consideration in modelling solvent entropy.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.