Solute generation

SoluteGenFlow

Bases: MartiniFlowProject

Manages the workflow for generating, minimizing, and equilibrating solute systems for molecular dynamics simulations.

This class extends MartiniFlowProject to provide specific functionalities for solute system preparation in the context of molecular dynamics simulations using GROMACS. It includes operations for generating the initial molecular structure, topology, and parameter files, minimizing the system's energy, and equilibrating the system under desired conditions.

Attributes:

Name	Type	Description
workspace_path	str	Path to the workspace directory where simulation files are stored.
mdp_path	str	Path to the directory containing MDP files for GROMACS simulations.
itp_files	dict	Dictionary mapping solute names to their respective ITP file paths.
mdp_files	dict	Dictionary mapping simulation types (e.g., 'minimize', 'equilibrate') to their MDP file paths.
simulation_settings	dict	Settings for the simulation, such as the number of threads.
system_name	str	The name of the system being simulated.
nomad_workflow	str	The name of the NOMAD workflow associated with this project.
state_names	dict	Dictionary mapping state names to their string representations.
ff_parameters	dict	Force field parameters used in generating the molecular structure.

The class provides methods for each step of the solute preparation process, including build, minimize, and equilibrate, as well as methods for managing the workflow's integration with the NOMAD database, such as upload_to_nomad.

Source code in martignac/workflows/solute_generation.py

class SoluteGenFlow(MartiniFlowProject):
    """
    Manages the workflow for generating, minimizing, and equilibrating solute systems for molecular dynamics simulations.

    This class extends `MartiniFlowProject` to provide specific functionalities for solute system preparation in the
    context of molecular dynamics simulations using GROMACS. It includes operations for generating the initial molecular
    structure, topology, and parameter files, minimizing the system's energy, and equilibrating the system under desired
    conditions.

    Attributes:
        workspace_path (str): Path to the workspace directory where simulation files are stored.
        mdp_path (str): Path to the directory containing MDP files for GROMACS simulations.
        itp_files (dict): Dictionary mapping solute names to their respective ITP file paths.
        mdp_files (dict): Dictionary mapping simulation types (e.g., 'minimize', 'equilibrate') to their MDP file paths.
        simulation_settings (dict): Settings for the simulation, such as the number of threads.
        system_name (str): The name of the system being simulated.
        nomad_workflow (str): The name of the NOMAD workflow associated with this project.
        state_names (dict): Dictionary mapping state names to their string representations.
        ff_parameters (dict): Force field parameters used in generating the molecular structure.

    The class provides methods for each step of the solute preparation process, including `build`, `minimize`, and
    `equilibrate`, as well as methods for managing the workflow's integration with the NOMAD database, such as
    `upload_to_nomad`.
    """

    workspace_path: str = (
        f"{MartiniFlowProject.workspaces_path}/{conf['relative_paths']['workspaces']}"
    )
    mdp_path = (
        f"{MartiniFlowProject.input_files_path}/{conf['relative_paths']['mdp_files']}"
    )
    itp_files = {k: v.get(str) for k, v in conf["itp_files"].items()}
    mdp_files = {k: v.get(str) for k, v in conf["mdp_files"].items()}
    simulation_settings = {"n_threads": conf["settings"]["n_threads"].get(int)}
    system_name = conf["output_names"]["system"].get(str)
    nomad_workflow: str = conf["output_names"]["nomad_workflow"].get(str)
    state_names = {k: v.get(str) for k, v in conf["output_names"]["states"].items()}
    ff_parameters = {
        "number_excl": conf["parameters"]["number_excl"].get(int),
        "bond_length": conf["parameters"]["bond_length"].get(float),
        "bond_constant": conf["parameters"]["bond_constant"].get(float),
    }

build(job)

Generate the initial structure, topology, and parameter files for a solute.

This function is responsible for generating the initial molecular structure (GRO file), topology (TOP file), and parameter (ITP file) files for the solute specified in the job. It utilizes the get_molecule_from_name function to fetch the molecular data based on the solute name provided in the job's state point. The generated files are essential for conducting molecular dynamics simulations using GROMACS.

The function updates the job document with paths to the generated files, marking the solute's initial system generation as complete. This step is crucial for preparing the system for subsequent energy minimization, equilibration, and production simulations.

Parameters:

Name	Type	Description	Default
job	Job	The job object representing the solute system for which the initial structure, topology, and parameter files are to be generated.	required

Returns:

Name	Type	Description
None	None	This function does not return a value but updates the job document with the paths to the generated files.

Source code in martignac/workflows/solute_generation.py

@SoluteGenFlow.pre(fetched_from_nomad)
@SoluteGenFlow.post(system_generated, tag="system_generated")
@SoluteGenFlow.operation_hooks.on_success(store_task)
@SoluteGenFlow.operation(with_job=True)
def build(job: Job) -> None:
    """
    Generate the initial structure, topology, and parameter files for a solute.

    This function is responsible for generating the initial molecular structure (GRO file),
    topology (TOP file), and parameter (ITP file) files for the solute specified in the job.
    It utilizes the `get_molecule_from_name` function to fetch the molecular data based on the
    solute name provided in the job's state point. The generated files are essential for
    conducting molecular dynamics simulations using GROMACS.

    The function updates the job document with paths to the generated files, marking the
    solute's initial system generation as complete. This step is crucial for preparing the
    system for subsequent energy minimization, equilibration, and production simulations.

    Args:
        job (Job): The job object representing the solute system for which the initial
                   structure, topology, and parameter files are to be generated.

    Returns:
        None: This function does not return a value but updates the job document with the
              paths to the generated files.
    """
    molecule = get_molecule_from_name(
        job.sp.solute_name,
        bond_length=SoluteGenFlow.ff_parameters["bond_length"],
        bond_constant=SoluteGenFlow.ff_parameters["bond_constant"],
        number_excl=SoluteGenFlow.ff_parameters["number_excl"],
    )
    generate_gro_file_for_molecule(
        molecule, SoluteGenFlow.get_state_name("generate", "gro")
    )
    generate_itp_file_for_molecule(molecule, SoluteGenFlow.get_state_name("", "itp"))
    generate_top_file_for_molecule(
        molecule,
        [*SoluteGenFlow.itp_files.values(), SoluteGenFlow.get_state_name("", "itp")],
        SoluteGenFlow.get_state_name("", "top"),
    )
    job.doc[project_name]["solute_itp"] = SoluteGenFlow.get_state_name("", "itp")
    job.doc[project_name]["solute_top"] = SoluteGenFlow.get_state_name("", "top")
    job.doc[project_name]["solute_name"] = molecule.name
    job.doc[project_name]["solute_has_charged_beads"] = molecule.has_charged_beads
    return None

equilibrate(job)

Perform the equilibration process for the solute in the simulation.

This function runs the GROMACS equilibration simulation using the parameters defined in the mdp_files["equilibrate"] file. It sets up the simulation with the minimized structure from the previous step as the input configuration and uses the topology file generated during the solute generation step. The number of threads for the simulation is determined by the simulation_settings["n_threads"] configuration.

The equilibration process is crucial for stabilizing the system at the desired temperature and pressure before the main production run. It helps in relaxing the system and achieving a more realistic distribution of velocities and positions.

Upon successful completion, the function updates the job document with the path to the generated GRO file, marking the state of the system as equilibrated.

Parameters:

Name	Type	Description	Default
job	Job	The job object for which the equilibration simulation is to be performed.	required

Returns:

Name	Type	Description
str	str	The command to execute the GROMACS equilibration simulation.

Source code in martignac/workflows/solute_generation.py

@SoluteGenFlow.pre(system_minimized, tag="system_minimized")
@SoluteGenFlow.post(system_equilibrated, tag="system_equilibrated")
@SoluteGenFlow.operation_hooks.on_success(store_gromacs_log_to_doc)
@SoluteGenFlow.operation(cmd=True, with_job=True)
def equilibrate(job: Job) -> str:
    """
    Perform the equilibration process for the solute in the simulation.

    This function runs the GROMACS equilibration simulation using the parameters defined in the
    `mdp_files["equilibrate"]` file. It sets up the simulation with the minimized structure from the previous step as
    the input configuration and uses the topology file generated during the solute generation step. The number of
    threads for the simulation is determined by the `simulation_settings["n_threads"]` configuration.

    The equilibration process is crucial for stabilizing the system at the desired temperature and pressure before the
    main production run. It helps in relaxing the system and achieving a more realistic distribution of velocities and
    positions.

    Upon successful completion, the function updates the job document with the path to the generated GRO file, marking
    the state of the system as equilibrated.

    Args:
        job (Job): The job object for which the equilibration simulation is to be performed.

    Returns:
        str: The command to execute the GROMACS equilibration simulation.
    """
    job.doc[project_name]["solute_gro"] = SoluteGenFlow.get_state_name(
        "equilibrate", "gro"
    )
    return gromacs_simulation_command(
        mdp=SoluteGenFlow.mdp_files["equilibrate"],
        top=SoluteGenFlow.get_state_name("", "top"),
        gro=SoluteGenFlow.get_state_name("minimize", "gro"),
        name=SoluteGenFlow.get_state_name("equilibrate"),
        n_threads=SoluteGenFlow.simulation_settings["n_threads"],
    )

minimize(job)

Minimize the energy of the solute system.

This function executes the energy minimization step for the solute using GROMACS. It utilizes the parameters specified in the mdp_files["minimize"] file for the minimization process. The minimized structure serves as a more stable starting point for subsequent equilibration and production simulations.

The minimization process reduces the potential energy of the system, resolving any steric clashes or unrealistic geometries that may have arisen during the solute generation phase. This step is crucial for preparing the system for a stable simulation environment.

Upon completion, the function updates the job document with the path to the minimized structure, indicating that the system has been successfully minimized.

Parameters:

Name	Type	Description	Default
job	Job	The job object representing the solute system to be minimized.	required

Returns:

Name	Type	Description
str	str	The command to execute the GROMACS energy minimization.

Source code in martignac/workflows/solute_generation.py

@SoluteGenFlow.pre(system_generated, tag="system_generated")
@SoluteGenFlow.post(system_minimized, tag="system_minimized")
@SoluteGenFlow.operation_hooks.on_success(store_gromacs_log_to_doc)
@SoluteGenFlow.operation(cmd=True, with_job=True)
def minimize(job: Job) -> str:
    """
    Minimize the energy of the solute system.

    This function executes the energy minimization step for the solute using GROMACS. It utilizes the parameters
    specified in the `mdp_files["minimize"]` file for the minimization process. The minimized structure serves as a
    more stable starting point for subsequent equilibration and production simulations.

    The minimization process reduces the potential energy of the system, resolving any steric clashes or unrealistic
    geometries that may have arisen during the solute generation phase. This step is crucial for preparing the system
    for a stable simulation environment.

    Upon completion, the function updates the job document with the path to the minimized structure, indicating that
    the system has been successfully minimized.

    Args:
        job (Job): The job object representing the solute system to be minimized.

    Returns:
        str: The command to execute the GROMACS energy minimization.
    """
    return gromacs_simulation_command(
        mdp=SoluteGenFlow.mdp_files["minimize"],
        top=SoluteGenFlow.get_state_name("", "top"),
        gro=SoluteGenFlow.get_state_name("generate", "gro"),
        name=SoluteGenFlow.get_state_name("minimize"),
        n_threads=SoluteGenFlow.simulation_settings["n_threads"],
    )