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PACKMOL

generate_solvent_with_packmol(gro_solvent_mol, box_length, output_pdb, packmol_input_file='packmol.inp')

Generates a solvent box with specified dimensions using PACKMOL.

This function converts a GROMACS .gro file of a solvent molecule to a .pdb file, calculates the number of molecules needed to fill a box of the given volume, and generates a PACKMOL input file to create a solvent box. The function then returns the command to run PACKMOL with the generated input file.

Parameters:

Name Type Description Default
gro_solvent_mol str

Path to the .gro file of the solvent molecule.

 required
box_length float

Length of the cubic box in nm to be filled with solvent molecules.

 required
output_pdb str

Path where the output .pdb file containing the solvent box should be saved.

 required
packmol_input_file str

Path to the PACKMOL input file to be generated. Defaults to "packmol.inp".

 'packmol.inp'

Returns:

Name Type Description
str str

The command to run PACKMOL with the generated input file.
Note

PACKMOL must be installed and accessible from the command line to execute the returned command successfully.

Source code in martignac/utils/packmol.py 
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def generate_solvent_with_packmol(
    gro_solvent_mol: str,
    box_length: float,
    output_pdb: str,
    packmol_input_file: str = "packmol.inp",
) -> str:
    """
    Generates a solvent box with specified dimensions using PACKMOL.

    This function converts a GROMACS .gro file of a solvent molecule to a .pdb file, calculates the number of molecules
    needed to fill a box of the given volume, and generates a PACKMOL input file to create a solvent box. The function
    then returns the command to run PACKMOL with the generated input file.

    Parameters:
        gro_solvent_mol (str): Path to the .gro file of the solvent molecule.
        box_length (float): Length of the cubic box in nm to be filled with solvent molecules.
        output_pdb (str): Path where the output .pdb file containing the solvent box should be saved.
        packmol_input_file (str, optional): Path to the PACKMOL input file to be generated. Defaults to "packmol.inp".

    Returns:
        str: The command to run PACKMOL with the generated input file.

    Note:
        PACKMOL must be installed and accessible from the command line to execute the returned command successfully.
    """
    pdb_solvent_mol = f"{gro_solvent_mol.rstrip('.gro')}.pdb"
    universe = Universe(gro_solvent_mol)
    universe.atoms.write(pdb_solvent_mol)
    length_in_a = box_length * 10.0
    num_beads_per_mol = len(universe.residues[0].atoms)
    volume_box = box_length**3
    num_beads_in_box = int(volume_box / (num_beads_per_mol * VOLUME_PER_CG_BEAD_IN_NM3))
    logger.info(f"calling packmol to generate box with {num_beads_in_box} molecules")
    packmol_inp = f"""tolerance 2.0
filetype pdb
output {output_pdb}

structure {pdb_solvent_mol}
  number {num_beads_in_box}
  inside box 0. 0. 0. {length_in_a} {length_in_a} {length_in_a}
end structure
"""
    with open(packmol_input_file, "w") as pipe:
        pipe.write(packmol_inp)
    return f"packmol < {packmol_input_file}"

place_solute_in_solvent_with_packmol(gro_solute, gro_solvent, output_pdb, restraint_along_x=None, restraint_along_y=None, restraint_along_z=None, restraint_std_dev=1.0, packmol_input_file='packmol.inp')

Places a solute molecule within a solvent box using PACKMOL with optional positional restraints.

This function prepares a PACKMOL input file to place a solute molecule within a pre-existing solvent box, allowing for the specification of positional restraints along the x, y, and z axes. This can be particularly useful for simulations where the solute needs to be positioned at a specific location within the solvent box, such as near a surface or interface. The function returns the command to run PACKMOL with the generated input file.

Parameters:

Name Type Description Default
gro_solute str

Path to the .gro file of the solute molecule.

 required
gro_solvent str

Path to the .gro file of the solvent box.

 required
output_pdb str

Path where the output .pdb file, containing both solute and solvent, should be saved.

 required
restraint_along_x Optional[float]

Optional x-coordinate to restrain the solute molecule along the x-axis.

 None
restraint_along_y Optional[float]

Optional y-coordinate to restrain the solute molecule along the y-axis.

 None
restraint_along_z Optional[float]

Optional z-coordinate to restrain the solute molecule along the z-axis.

 None
restraint_std_dev float

Standard deviation for the positional restraint, defining the allowed fluctuation range.

 1.0
packmol_input_file str

Path to the PACKMOL input file to be generated. Defaults to "packmol.inp".

 'packmol.inp'

Returns:

Name Type Description
str str

The command to run PACKMOL with the generated input file.
Note

PACKMOL must be installed and accessible from the command line to execute the returned command successfully.

Source code in martignac/utils/packmol.py 
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def place_solute_in_solvent_with_packmol(
    gro_solute: str,
    gro_solvent: str,
    output_pdb: str,
    restraint_along_x: Optional[float] = None,
    restraint_along_y: Optional[float] = None,
    restraint_along_z: Optional[float] = None,
    restraint_std_dev: float = 1.0,
    packmol_input_file: str = "packmol.inp",
) -> str:
    """
    Places a solute molecule within a solvent box using PACKMOL with optional positional restraints.

    This function prepares a PACKMOL input file to place a solute molecule within a pre-existing solvent box,
    allowing for the specification of positional restraints along the x, y, and z axes. This can be particularly
    useful for simulations where the solute needs to be positioned at a specific location within the solvent box,
    such as near a surface or interface. The function returns the command to run PACKMOL with the generated input file.

    Parameters:
        gro_solute (str): Path to the .gro file of the solute molecule.
        gro_solvent (str): Path to the .gro file of the solvent box.
        output_pdb (str): Path where the output .pdb file, containing both solute and solvent, should be saved.
        restraint_along_x (Optional[float]): Optional x-coordinate to restrain the solute molecule along the x-axis.
        restraint_along_y (Optional[float]): Optional y-coordinate to restrain the solute molecule along the y-axis.
        restraint_along_z (Optional[float]): Optional z-coordinate to restrain the solute molecule along the z-axis.
        restraint_std_dev (float): Standard deviation for the positional restraint, defining the allowed fluctuation range.
        packmol_input_file (str): Path to the PACKMOL input file to be generated. Defaults to "packmol.inp".

    Returns:
        str: The command to run PACKMOL with the generated input file.

    Note:
        PACKMOL must be installed and accessible from the command line to execute the returned command successfully.
    """
    logger.info("calling packmol to place solute in solvent")
    pdb_solute = f"{gro_solute.rstrip('.gro')}.pdb"
    universe = Universe(gro_solute)
    universe.atoms.write(pdb_solute)
    pdb_solvent = f"{gro_solvent.rstrip('.gro')}.pdb"
    universe = Universe(gro_solvent)
    universe.atoms.write(pdb_solvent)
    box_dimensions = universe.dimensions
    logger.info(f"box dimensions: {box_dimensions}")
    x_min, x_max = 0.0, box_dimensions[0]
    if restraint_along_x is not None:
        x_min = restraint_along_x - restraint_std_dev
        x_max = restraint_along_x + restraint_std_dev
    y_min, y_max = 0.0, box_dimensions[1]
    if restraint_along_y is not None:
        y_min = restraint_along_y - restraint_std_dev
        y_max = restraint_along_y + restraint_std_dev
    z_min, z_max = 0.0, box_dimensions[2]
    if restraint_along_z is not None:
        z_min = restraint_along_z - restraint_std_dev
        z_max = restraint_along_z + restraint_std_dev
    packmol_inp = f"""tolerance 2.0

filetype pdb

output {output_pdb}

structure {pdb_solvent}
  number 1
  fixed 0. 0. 0. 0. 0. 0.
end structure

structure {pdb_solute}
  number 1
  inside box {x_min} {y_min} {z_min} {x_max} {y_max} {z_max}
end structure
"""
    with open(packmol_input_file, "w") as pipe:
        pipe.write(packmol_inp)
    return f"packmol < {packmol_input_file}"