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References

Primary citations

If this package was useful to you, please cite the following papers:

  • L. Martínez, ComplexMixtures.jl: Investigating the structure of solutions of complex-shaped molecules from a solvent-shell perspective. J. Mol. Liq. 347, 117945, 2022. [Full Text]

  • L. Martínez, S. Shimizu, Molecular interpretation of preferential interactions in protein solvation: a solvent-shell perspective by means of minimum-distance distribution functions. J. Chem. Theor. Comp. 13, 6358–6372, 2017. [Full Text]

Applications and examples

  • F. C. Ramos, L. Martínez, Molecular dynamics and solvation structures of the β-glucosidase from Humicola insolens (BGHI) in aqueous solutions containing glucose Int. J. Biol. Macromol. 2024. [Full Text]

  • V. Piccoli, L. Martínez, Competitive Effects of Anions on Protein Solvation by Aqueous Ionic Liquids. J. Phys. Chem. B 128, 7792-7802, 2024. [Full Text]

  • A. F. Pereira, L. Martínez, Helical Content Correlations and Hydration Structures of the Folding Ensemble of the B Domain of Protein A. J. Chem. Inf. Model. 64, 3350-3359, 2024. [Full Text]

  • A. F. Pereira, V. Piccoli, L. Martínez, Trifluoroethanol direct interactions with protein backbones destabilize alpha-helices. J. Mol. Liq. 365, 120209, 2022. [Full Text]

  • V. Piccoli, L. Martínez, Ionic liquid solvation of proteins in native and denatured states. J. Mol. Liq. 363, 119953, 2022. [Full Text]

  • V. Piccoli, L. Martínez, Correlated counterion effects in the solvation of proteins by ionic-liquids. J. Mol. Liq. 320, 114347, 2020. [Full Text]

  • I. P. de Oliveira, L. Martínez, The shift in urea orientation at protein surfaces at low pH is compatible with a direct mechanism of protein denaturation. Phys. Chem. Chem. Phys. 22, 354-367, 2020. [Full Text]

  • I. P. de Oliveira, L. Martínez, Molecular basis for competitive solvation of the Burkholderia cepacia lipase by sorbitol and urea. Phys. Chem. Chem. Phys. 18, 21797-21808, 2016. [Full Text]

See also

  • Packmol: A package for building initial configurations for molecular dynamics simulations.

  • CellListMap.jl: Efficient and customizable implementation of cell lists, which allows the computation of general properties dependent on distances of particles within a cutoff, for example short-range potentials, forces, neighbor lists, etc.

  • MDLovoFit: Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis.

Breaking changes

The syntax changes necessary to update script from version 1.X to 2.X of the package are:

Atom selections

The previous Selection structure was renamed to AtomSelection for clarity.

  • Before:
water = Selection(water; natomspermol=3)
  • Now:
water = AtomSelection(water; natomspermol=3)

Group contributions syntax

The syntax to computing group contributions is improved. Previously, the contrib or contributions functions required three somewhat redundant parameters.

  • Before:

The call to contributions required 3 parameters: the Selection structure, the matrix of contributions, and the indexes of the atoms for which the contributions were desired:

h_contributions = contributions(solvent, R.solvent_atom, h_indexes)
  • Now:

The contributions are extracted from the Result data structure, by providing either a SoluteGroup or SolventGroup object, which are setup with the group names, group indexes, atom names, or atom indexes:

h_contributions = contributions(R, SolventGroup(h_indexes))

Frame weights

frame_weights is an option of the mddf execution. That is previously, they were defined in the Options data structure, and now they are passed to the mddf function.

  • Before:
options = Options(frame_weights=[1.0, 2.0], bulk_range=(8.0, 12.0))
results = mddf(trajectory_file, solute, solvent, options)
  • Now:
results = mddf(trajectory_file, solute, solvent, options; frame_weights=[1.0, 2.0])