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 1.3.3) the module supports the construction of systems of a solute solvated by a mixture of two solvents.

How to use it

julia> using MolSimToolkit.PackmolInputCreator

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
)

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.

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, 
    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. 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.

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 file system.pdb will be generated.

Help entries

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")

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

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
)