System setup

Packmol Input Creator

This module helps the setup of a Packmol input file, by computing the number of molecules and sizes necessary to build different systems. Currently (as of version 1.27.0) the module supports the construction of systems of a solute (macromolecule for example) solvated by a a single solvent or a mixture of two solvents.

• Solute-Solvent system
• Solute-Solvent-Cossolvent system

How to use it

julia> using MolSimToolkit.PackmolInputCreator

Running Packmol

Packmol can be run directly from within Julia using the Packmol Julia package:

using Packmol
run_packmol("./box.inp")

If everything runs correctly, the output PDB file of the system will be created.

Solute-Solvent system

Here, SolutionBoxUS stands for Solute (U) and Solvent (S). The density of the solvent can be one of "g/mL" or "mol/L" (molarity).

SolutionBoxUS(; 
    solute_pdbfile::String, 
    solvent_pdbfile::String,
    density::Float64,
    density_units = "g/mL",
    solute_molar_mass = nothing, # optional
    solvent_molar_mass = nothing, # optional
)

write_packmol_input(
    system::SolutionBoxUS;
    input="box.inp",
    output="system.pdb",
    # box size
    box_sides::AbstractVector{<:Real}, # or
    margin::Real,
    cubic::Bool = false,
)

Setting up the system properties

We initialize the system data structure, given the PDB files of one molecule of the polymer (poly_h.pdb), and one molecule of water:

# Directory of test files
test_dir = MolSimToolkit.PackmolInputCreator.PackmolInputCreatorDirectory*"/test"
# Construction of system data structure
system = SolutionBoxUSC(
    solute_pdbfile = "$test_dir/data/poly_h.pdb",
    solvent_pdbfile = "$test_dir/data/water.pdb",
    density = 1.0,
    density_units = "g/mL",
    solute_molar_mass = nothing, # optional
    solvent_molar_mass = nothing, # optional
)

The molar masses of the components can be provided explicitly by the user. If not, they will be computed from the atom types in the PDB files, but this may fail if the mass of some atom type is unknown.

Finally, we can generate an input file for Packmol with:

write_packmol_input(
    system; 
    margin = 20.0, 
    cubic = true,
    input = "box.inp",
    output = "system.pdb"
)

The input parameter provides the name of the input file for Packmol that will be generated.

The margin parameter sets the size of the box, which will take into consideration the maximum and minimum dimensions of the solute. If cubic is set to true the box will be cubic, otherwise it will be orthorhombic but with different length in each direction, respecting the margin provided.

Alternatively, the size of the box can be provided explicitly with the box_sides = [ a, b, c ] parameters, where a, b, and c are the lengths of the box in each dimension.

Solute-Solvent-Cossolvent system

Here, SolutionBoxUSC stands for Solute (U), Solvent (S), and Cossolvent (C). The concentration units can be one of "mol/L" (molarity), "x" (molar fraction), "vv" (volume fraction), and "mm" (mass fraction). The density is assumed to be in g/mL.

SolutionBoxUSC(; 
    solute_pdbfile::String, 
    solvent_pdbfile::String,
    cossolvent_pdbfile::String,
    density_table::Matrix{Float64},
    concentration_units = "x",
    solute_molar_mass = nothing, # optional
    solvent_molar_mass = nothing, # optional
    cossolvent_molar_mass = nothing, # optional
)

write_packmol_input(
    system::SolutionBoxUSC;
    concentration::Real, 
    input="box.inp",
    output="system.pdb",
    # box size
    box_sides::AbstractVector{<:Real}, # or
    margin::Real,
    cubic::Bool = false,
)

convert_concentration(
    system::SolutionBoxUSC,
    input_concentration, 
    units
)

convert_concentration(system, 55.5, "mol/L" => "x")

convert_density_table!(system::SolutionBoxUSC, target_units)

convert_density_table!(system, "mol/L")

Setting up the system properties

Here, we setup a system of a polymer solvated by water and ethanol. The densities as a function of the molar fraction of ethanol are available in a data table:

density_table = [
# x cossolvent (ethanol)     density (g/mL)
         0.0000                 0.9981
         0.0416                 0.9820
         0.0890                 0.9685
         0.1434                 0.9537
         0.2066                 0.9369
         0.2809                 0.9151
         0.3695                 0.8923
         0.4769                 0.8685
         0.6098                 0.8450
         0.7786                 0.8195
         1.0000                 0.7906
]

Next, we initialize the system data structure, given the PDB files of one molecule of the polymer (poly_h.pdb), and one molecule of water and ethanol:

# Directory of test files
test_dir = MolSimToolkit.PackmolInputCreator.PackmolInputCreatorDirectory*"/test"
# Construction of system data structure
system = SolutionBoxUSC(
    solute_pdbfile = "$test_dir/data/poly_h.pdb",
    solvent_pdbfile = "$test_dir/data/water.pdb",
    cossolvent_pdbfile = "$test_dir/data/ethanol.pdb",
    density_table = density_table,
    concentration_units = "x", # molar fraction
    solute_molar_mass = nothing, # optional
    solvent_molar_mass = nothing, # optional
    cossolvent_molar_mass = nothing, # optional
)

The molar masses of the components can be provided explicitly by the user. If not, they will be computed from the atom types in the PDB files, but this may fail if the mass of some atom type is unknown.

julia> convert_density_table!(system, "mol/L")

Finally, we can generate an input file for Packmol with:

write_packmol_input(
    system; 
    concentration = 0.5,
    margin = 20.0, 
    cubic = true,
    input = "box.inp",
    output = "system.pdb"
)

The concentration can be given in molar fraction (x), molarity (mol/L), or volume fraction (vv).

The input parameter provides the name of the input file for Packmol that will be generated.

The margin parameter sets the size of the box, which will take into consideration the maximum and minimum dimensions of the solute. If cubic is set to true the box will be cubic, otherwise it will be orthorhombic but with different length in each direction, respecting the margin provided.

Alternatively, the size of the box can be provided explicitly with the box_sides = [ a, b, c ] parameters, where a, b, and c are the lengths of the box in each dimension.