ArticleJournal of molecular modeling2011
Effect of atom- and group-based truncations on biomolecules simulated with reaction-field electrostatics.
Article in Journal of molecular modeling, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- In Silico Models for Predicting Adsorption of Organic Pollutants on Atmospheric Nanoplastics by Combining Grand Canonical Monte Carlo/Density Functional Theory and Quantitative Structure Activity Relationship Approach.Nanomaterials (Basel, Switzerland) · 2026Article
- Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference.Biophysical reviews · 2022Review
- Testing for physical validity in molecular simulations.PloS one · 2018Article
- Molecular dynamics simulation of water permeation through the alpha-hemolysin channel.Journal of biological physics · 2016Article
- Classical electrostatics for biomolecular simulations.Chemical reviews · 2014Review
- Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.PloS one · 2013Article
- Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model.Communications in computational physics · 2013Article
- Non-Ewald methods: theory and applications to molecular systems.Biophysical reviews · 2012Article
- Microsecond molecular dynamics simulations of intrinsically disordered proteins involved in the oxidative stress response.PloS one · 2011Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The performance of the reaction-field method of electrostatics is tested in molecular dynamics simulations of protein human interleukin-4 and a short DNA fragment in explicit solvent. Two truncation schemes are considered: one based on the position of atomic charges in water molecules and the other on the position of groups of charges. The group-based truncation leads to the melting of the DNA double helix. In contrast, the atom-based truncation maintains the helical structure intact. Similarly for the protein, the group-based truncation leads to an unfolding at pH 2 while the atom-based truncation produces stable trajectories at low and normal pH, in agreement with experiment. Artificial repulsion between charged residues associated with the group-based truncation is identified as the microscopic reason behind unfolding of the protein. Implications of different truncation schemes in reaction-field simulations of biomolecules are discussed.
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