ArticleJournal of chemical theory and computation2018
SLTCAP: A Simple Method for Calculating the Number of Ions Needed for MD Simulation.
Article in Journal of chemical theory and computation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
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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.
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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.
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Who cites it
31 citing papers in PubMed.
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- Immunoinformatics-based design of a next generation multi-epitope vaccine candidate against Shigella boydii using a hierarchical subtractive proteomics approach.Scientific reports · 2025Article
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- Regulatory role of stem-loop structures in Faba bean necrotic yellows virus replication efficiency.Microbiology spectrum · 2025Article
- On the Photosensitizing Properties of Aloe-Emodin in Photodynamic Therapy: Insights from the Molecular Modeling.The journal of physical chemistry. B · 2025Article
- Application of Anomaly Detection to Identify Important Features of Protein Dynamics.ACS omega · 2025Article
- Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA.Journal of chemical theory and computation · 2024Article
- Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2024Article
- PTM-Psi: A python package to facilitate the computational investigation of post-translational modification on protein structures and their impacts on dynamics and functions.Protein science : a publication of the Protein Society · 2023Article
- Intrinsic disorder and conformational coexistence in auxin coreceptors.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Assessing the performance of docking, FEP, and MM/GBSA methods on a series of KLK6 inhibitors.Journal of computer-aided molecular design · 2023Article
- β-Sitosterol could serve as a dual inhibitor of Trypanosoma congolense sialidase and phospholipase AMolecular diversity · 2023Article
- Characterization of cytoskeletal and structural effects of INF2 variants causing glomerulopathy and neuropathy.Scientific reports · 2023Article
- The E2 glycoprotein holds key residues for Mayaro virus adaptation to the urban Aedes aegypti mosquito.PLoS pathogens · 2023Article
- Switching from Aromatase Inhibitors to Dual Targeting Flavonoid-Based Compounds for Breast Cancer Treatment.Molecules (Basel, Switzerland) · 2023Article
- Computer-Assisted Design and Characterization of RNA Nanostructures.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Predicting molecular properties of α-synuclein using force fields for intrinsically disordered proteins.Proteins · 2023Article
- Stomatal COScience advances · 2022Article
- Study of trioleoylglycerol two-layer and adiposome cross-section mimicking four-layer systems through atomic-level simulations.Structural dynamics (Melville, N.Y.) · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
An accurate depiction of electrostatic interactions in molecular dynamics requires the correct number of ions in the simulation box to capture screening effects. However, the number of ions that should be added to the box is seldom given by the bulk salt concentration because a charged biomolecule solute will perturb the local solvent environment. We present a simple method for calculating the number of ions that requires only the total solute charge, solvent volume, and bulk salt concentration as inputs. We show that the most commonly used method for adding salt to a simulation results in an effective salt concentration that is too high. These findings are confirmed using simulations of lysozyme. We have established a web server where these calculations can be readily performed to aid simulation setup.
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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.