ArticleJournal of chemical theory and computation2014
Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 11 citations in OpenAlex.
- The dynamics of linear polyubiquitin.Science advances · 2020Article
- Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations.Journal of chemical theory and computation · 2017Article
- An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase.Scientific reports · 2016Article
- Extracting water and ion distributions from solution x-ray scattering experiments.The Journal of chemical physics · 2016Article
- ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins.Journal of chemical theory and computation · 2014Article
- Thermodynamics of Deca-alanine Folding in Water.Journal of chemical theory and computation · 2014Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The description of aggregation processes with molecular dynamics simulations is a playground for testing biomolecular force fields, including a new generation of force fields that explicitly describe electronic polarization. In this work, we study a system consisting of 50 glycyl-l-alanine (Gly-Ala) dipeptides in solution with 1001 water molecules. Neutron diffraction experiments have shown that at this concentration, Gly-Ala aggregates into large clusters. However, general-purpose force fields in combination with established water models can fail to correctly describe this aggregation process, highlighting important deficiencies in how solute-solute and solute-solvent interactions are parametrized in these force fields. We found that even for the fully polarizable AMOEBA force field, the degree of association is considerably underestimated. Instead, a fixed point-charge approach based on the newly developed IPolQ scheme [Cerutti et al.
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Registered trials
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