ArticleJournal of computational chemistry2020
The effect of different cutoff schemes in molecular simulations of proteins.
Article in Journal of computational chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Which Metrics Best Capture Protein Structural Changes in Molecular Dynamics Simulations? Evaluating Score Combinations and Force-Field Effects.Journal of chemical information and modeling · 2026Article
- The Effect of CuACS chemical neuroscience · 2026Article
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS.Journal of computational chemistry · 2025Article
- On the Validation of Protein Force Fields Based on Structural Criteria.The journal of physical chemistry. B · 2024Article
- The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach.Journal of chemical information and modeling · 2024Article
- Experimental and Theoretical Brownian Dynamics Analysis of Ion Transport During Cellular Electroporation of E. coli Bacteria.Annals of biomedical engineering · 2024Article
- Comparative Study of Molecular Mechanics Force Fields for β-Peptidic Foldamers: Folding and Self-Association.Journal of chemical information and modeling · 2023Article
- On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins.Journal of computational chemistry · 2021Article
- EfficientJournal of chemical information and modeling · 2021Article
- Article
- The effect of different cutoff schemes in molecular simulations of proteins.Journal of computational chemistry · 2020Article
- The Effect of Using a Twin-Range Cutoff Scheme for Nonbonded Interactions: Implications for Force-Field Parametrization?Journal of chemical theory and computation · 2020Article
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2 authors.
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Abstract
Molecular simulations of nanoscale systems invariably involve assumptions and approximations to describe the electrostatic interactions, which are long-ranged in nature. One approach is the use of cutoff schemes with a reaction-field contribution to account for the medium outside the cutoff scheme. Recent reports show that macroscopic properties may depend on the exact choice of cutoff schemes in modern day simulations. In this work, a systematic analysis of the effects of different cutoff schemes was performed using a set of 52 proteins. We find no statistically significant differences between using a twin-range or a single-range cutoff scheme. Applying the cutoff based on charge groups or based on atomic positions, does lead to significant differences, which is traced to the cutoff noise for energies and forces. While group-based cutoff schemes show increased cutoff noise in the potential energy, applying an atomistic cutoff leads to artificial structure in the solvent at the cutoff distance. Carefully setting the temperature control, or using an atomistic cutoff for the solute and a group-based cutoff for the solvent significantly reduces the effects of the cutoff noise, without introducing structure in the solvent. This study aims to deepen the understanding of the implications different cutoffs have on molecular dynamics simulations.
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