Solvation and interactions

bulk_coordination(
    simulation::Simulation;
    reference_solute::AbstractVector{<:PDBTools.Atom}, 
    solute::AbstractVector{<:PDBTools.Atom},
    n_atoms_per_molecule_solute::Integer,
    solvent::AbstractVector{<:PDBTools.Atom}, 
    n_atoms_per_molecule_solvent::Integer,
    dmax::Real = 5.0,
    cutoff::Real = 20.0,
    bin_size::Real = 0.1,
    show_progress = true,
)

Computes the coordination number of one type of solvent molecule relative to another solvent molecule, as a function of the distance to a reference solute molecule.

For example, imagine a protein solvated in a mixture of water and TMAO. This function allows to compute the number of water molecules that are within a given distance to the TMAO molecules, as a function of the distance to the protein. That is, it computes the coordination number of water relative to TMAO, as a function of the distance to the protein.

The function returns the the distances and the histogram of the coordination number as a function of the distance.

Arguments

• simulation::Simulation: The simulation object
• reference_solute::AbstractVector{PDBTools.Atom}: The atoms of the reference solute molecule (the protein in the example above).
• solute::AbstractVector{PDBTools.Atom}: The atoms of the solute molecule (the TMAO in the example above).
• n_atoms_per_molecule_solute::Integer: The number of atoms per molecule of the solute.
• solvent::AbstractVector{PDBTools.Atom}: The atoms of the solvent molecule (the water in the example above).
• n_atoms_per_molecule_solvent::Integer: The number of atoms per molecule of the solvent.
• dmax::Real = 5.0: The maximum distance to the solute to consider a solvent molecule as coordinated.
• cutoff::Real = 20.0: The maximum distance to the reference molecule for computing the histogram.
• bin_size::Real = 0.1: The size of the bins for the histogram.
• show_progress = true: Whether to show a progress bar.

Example

julia> using MolSimToolkit, PDBTools

julia> pdb = readPDB(MolSimToolkit.Testing.namd2_pdb); # protein-tmao-water system

julia> trajectory = MolSimToolkit.Testing.namd2_traj;

julia> simulation = Simulation(pdb, trajectory)
Simulation 
    Atom type: Atom
    PDB file: -
    Trajectory file: /home/leandro/.julia/dev/MolSimToolkit/test/data/namd/protein_in_water_tmao/trajectory.dcd
    Total number of frames: 20
    Frame range: 1:1:20
    Number of frames in range: 20
    Current frame: nothing

julia> r, h = bulk_coordination(
           simulation;
           reference_solute = select(pdb, "protein"),
           solute = select(pdb, "resname TMAO"),
           n_atoms_per_molecule_solute = 14,
           solvent = select(pdb, "water"),
           n_atoms_per_molecule_solvent = 3,
       );

julia> using Plots

julia> plot(r, h, # plots `h` as a function of `r`
           xlabel = "Distance to protein (Å)",
           ylabel = "TMAO-water Coordination number",
           linewidth=2,
           label=:none, framestyle=:box, fontfamily="Computer Modern",
       )

coordination_number(
    sim::Simulation,
    solute::AbstractVector{<:PDBTools.Atom},
    solvent::AbstractVector{<:PDBTools.Atom};
    solvent_natomspermol::Integer,
    cutoff::Real,
    show_progress::Bool = true
)

Calculate the coordination number of the solute atoms with the solvent atoms.

Positional Arguments

• sim::Simulation: Simulation object.
• solute::AbstractVector{<:PDBTools.Atom}: Vector of solute atoms.
• solvent::AbstractVector{<:PDBTools.Atom}: Vector of solvent atoms.

Keyword Arguments

• solvent_natomspermol::Integer: Number of atoms per solvent molecule.
• cutoff::Real: Cutoff distance.
• show_progress::Bool: Show progress bar. (optional, default: true)

Returns

• cn::Vector{Int}: Vector with the coordination number of the solute atoms with the solvent atoms, at each frame.

Example

julia> using MolSimToolkit, PDBTools, MolSimToolkit.Testing

julia> sim = Simulation(Testing.namd2_pdb, Testing.namd2_traj; frames=1:5);

julia> protein = select(atoms(sim), "protein");

julia> tmao = select(atoms(sim), "resname TMAO");

julia> coordination_number(sim, protein, tmao; solvent_natomspermol=14, cutoff=3.0, show_progress=false)
5-element Vector{Int64}:
 7
 3
 4
 5
 6