ArticleThe journal of physical chemistry letters2022
Constant pH Coarse-Grained Molecular Dynamics with Stochastic Charge Neutralization.
Article in The journal of physical chemistry letters, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 19 citations in OpenAlex.
- Secondary Structure Bead-Encoded Amphiphilicity Biases Peptide Self-Assembly Prediction in MARTINI Coarse-Grained Simulations.ACS applied materials & interfaces · 2026Article
- Effects of doping and functionalization on black phosphorus nanosheets for enhanced quercetin delivery.RSC advances · 2025Article
- Article
- Biomolecular Condensates as Emerging Biomaterials: Functional Mechanisms and Advances in Computational and Experimental Approaches.Advanced materials (Deerfield Beach, Fla.) · 2025Review
- Challenges in simulating whole virus particles and how to fix them with the SIRAH force field.Biophysical reviews · 2025Review
- Review
- An active machine learning discovery platform for membrane-disrupting and pore-forming peptides.Physical chemistry chemical physics : PCCP · 2024Article
- Assessment of the MARTINI 3 Performance for Short Peptide Self-Assembly.Journal of chemical theory and computation · 2024Article
- Short Peptide Self-Assembly in the Martini Coarse-Grain Force Field Family.Accounts of chemical research · 2023Article
- Constant pH molecular dynamics simulations: Current status and recent applications.Current opinion in structural biology · 2022Review
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
pH dependence abounds in biochemical systems; however, many simulation methods used to investigate these systems do not consider this property. Using a modified version of the hybrid non-equilibrium molecular dynamics (MD)/Monte Carlo algorithm, we include a stochastic charge neutralization method, which is particularly suited to the MARTINI force field and enables artifact-free Ewald summation methods in electrostatic calculations. We demonstrate the efficacy of this method by reproducing pH-dependent self-assembly and self-organization behavior previously reported in experimental literature. In addition, we have carried out experimental oleic acid titrations where we report the results in a more relevant way for the comparison with computational methods than has previously been done.
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