iphasimulator.simulation_gromacs_runner

Generate GROMACS run folders and command templates.

Classes

`GromacsRunFiles`	Files generated for a staged GROMACS run.
`GromacsPreparedRunFolder`	Files generated for a GROMACS run folder.
`GromacsTopologyValidation`	Validation result for GROMACS topology include files.
`GromacsLocalMinimizationCheck`	Files and command needed to run local GROMACS minimisation.
`GromacsBoxValidation`	Box-size validation against GROMACS nonbonded cutoffs.
`GromacsSolvationFiles`	Files generated for the standard GROMACS solvate/genion workflow.
`GromacsSolvatedTopologyValidation`	Water and ion molecule counts parsed from a GROMACS topology.
`GromacsGromppValidation`	Result of a lightweight GROMACS `grompp` validation command.
`GromacsCoordinateTopologyValidation`	Atom-count comparison between a GRO coordinate file and topology.

Functions

`write_gromacs_run_files`(→ GromacsRunFiles)	Write basic GROMACS `mdp` files and a staged run script.
`create_gromacs_simulation_box`(→ pathlib.Path)	Create a centered GROMACS simulation box with `gmx editconf`.
`validate_gromacs_box_against_mdp`(→ GromacsBoxValidation)	Warn when a GRO box is too small for the MDP nonbonded cutoffs.
`count_gro_atoms`(→ int)	Read the atom count from the second line of a GROMACS `.gro` file.
`validate_gromacs_coordinate_topology_counts`(...)	Compare final coordinate atoms with topology molecule atom counts.
`write_gromacs_solvation_files`(→ GromacsSolvationFiles)	Write files for the standard GROMACS solvate/genion workflow.
`validate_gromacs_solvated_topology`(...)	Validate that topology molecule counts include solvent and ions.
`validate_gromacs_solvation_grompp`(...)	Run the two `grompp` checks required by the solvation workflow.
`validate_gromacs_run_folder`(→ GromacsTopologyValidation)	Validate external include files referenced by a GROMACS topology.
`check_gromacs_minimization_inputs`(...)	Check the files needed before running local GROMACS minimisation.
`run_gromacs_local_minimization`(...)	Run the local minimisation script from inside the GROMACS folder.
`prepare_gromacs_run_folder`(→ GromacsPreparedRunFolder)	Prepare self-contained GROMACS workflow folders from AMBER files.

Module Contents

class iphasimulator.simulation_gromacs_runner.GromacsRunFiles

Files generated for a staged GROMACS run.

output_dir: pathlib.Path

minim_mdp_path: pathlib.Path

nvt_mdp_path: pathlib.Path

npt_mdp_path: pathlib.Path

production_mdp_path: pathlib.Path

run_script_path: pathlib.Path

class iphasimulator.simulation_gromacs_runner.GromacsPreparedRunFolder

Files generated for a GROMACS run folder.

output_dir: pathlib.Path

workflow_type: str

dry_polymer_dir: pathlib.Path

solvated_polymer_dir: pathlib.Path

charmm_gui_membrane_dir: pathlib.Path

step5_input_gro_path: pathlib.Path

topol_top_path: pathlib.Path

index_ndx_path: pathlib.Path

mdp_paths: tuple[pathlib.Path, ...]

local_script_path: pathlib.Path

hpc_script_path: pathlib.Path

charmm_gui_membrane_hpc_script_path: pathlib.Path

class iphasimulator.simulation_gromacs_runner.GromacsTopologyValidation

Validation result for GROMACS topology include files.

topol_top_path: pathlib.Path

is_standalone: bool

included_files: tuple[pathlib.Path, ...]

missing_files: tuple[pathlib.Path, ...]

property valid: bool

class iphasimulator.simulation_gromacs_runner.GromacsLocalMinimizationCheck

Files and command needed to run local GROMACS minimisation.

output_dir: pathlib.Path

required_files: tuple[pathlib.Path, ...]

missing_files: tuple[pathlib.Path, ...]

command: tuple[str, ...]

property ready: bool

property command_text: str

class iphasimulator.simulation_gromacs_runner.GromacsBoxValidation

Box-size validation against GROMACS nonbonded cutoffs.

gro_path: pathlib.Path

mdp_path: pathlib.Path

box_vectors_nm: tuple[float, ...]

shortest_box_vector_nm: float

cutoffs_nm: dict[str, float]

property max_cutoff_nm: float | None

property valid: bool

class iphasimulator.simulation_gromacs_runner.GromacsSolvationFiles

Files generated for the standard GROMACS solvate/genion workflow.

output_dir: pathlib.Path

ions_mdp_path: pathlib.Path

solvation_itp_paths: tuple[pathlib.Path, ...]

solvent_itp_path: pathlib.Path

cation_itp_path: pathlib.Path

anion_itp_path: pathlib.Path

solvate_script_path: pathlib.Path

local_script_path: pathlib.Path

hpc_script_path: pathlib.Path

charmm_gui_membrane_hpc_script_path: pathlib.Path

property tip3p_ions_itp_path: pathlib.Path: Backward-compatible alias for older callers.

class iphasimulator.simulation_gromacs_runner.GromacsSolvatedTopologyValidation

Water and ion molecule counts parsed from a GROMACS topology.

topol_top_path: pathlib.Path

molecule_counts: dict[str, int]

water_count: int

cation_count: int

anion_count: int

property sodium_count: int: Backward-compatible alias; may include POT/K in newer workflows.

property chloride_count: int: Backward-compatible alias for anion count.

property has_water: bool

property has_ions: bool

class iphasimulator.simulation_gromacs_runner.GromacsGromppValidation

Result of a lightweight GROMACS grompp validation command.

command: tuple[str, ...]

returncode: int

stdout: str

stderr: str

property ok: bool

class iphasimulator.simulation_gromacs_runner.GromacsCoordinateTopologyValidation

Atom-count comparison between a GRO coordinate file and topology.

gro_path: pathlib.Path

topol_top_path: pathlib.Path

coordinate_atom_count: int

molecule_counts: dict[str, int]

molecule_atom_counts: dict[str, int]

expected_atom_count: int | None

property can_compare: bool

property valid: bool

iphasimulator.simulation_gromacs_runner.GROMACS_POLYMER_MDP_TEMPLATE_NAMES = ('step6.0_minimization.mdp', 'step6.1_nvt.mdp', 'step6.2_npt.mdp', 'step7_production.mdp')

iphasimulator.simulation_gromacs_runner.GROMACS_CHARMM_GUI_MEMBRANE_MDP_TEMPLATE_NAMES = ('step6.0_minimization.mdp', 'step6.1_equilibration.mdp', 'step6.2_equilibration.mdp',...

iphasimulator.simulation_gromacs_runner.GROMACS_MDP_TEMPLATE_NAMES = ('step6.0_minimization.mdp', 'step6.1_nvt.mdp', 'step6.2_npt.mdp', 'step7_production.mdp')

iphasimulator.simulation_gromacs_runner.GROMACS_ALL_MDP_TEMPLATE_NAMES = ('step6.0_minimization.mdp', 'step6.1_nvt.mdp', 'step6.2_npt.mdp', 'step7_production.mdp',...

iphasimulator.simulation_gromacs_runner.GROMACS_WORKFLOW_MDP_TEMPLATE_NAMES

iphasimulator.simulation_gromacs_runner.INCLUDE_PATTERN

iphasimulator.simulation_gromacs_runner.LOCAL_MINIMIZATION_REQUIRED_FILENAMES = ('step5_input.gro', 'topol.top', 'index.ndx', 'step6.0_minimization.mdp', 'run_step6_local.sh')

iphasimulator.simulation_gromacs_runner.MDP_CUTOFF_KEYS = ('rlist', 'rcoulomb', 'rvdw')

iphasimulator.simulation_gromacs_runner.WATER_MOLECULE_NAMES = ('SOL', 'WAT', 'TIP3', 'TIP3P', 'HOH')

iphasimulator.simulation_gromacs_runner.CATION_MOLECULE_NAMES = ('SOD', 'NA', 'NA+', 'POT', 'K', 'K+')

iphasimulator.simulation_gromacs_runner.ANION_MOLECULE_NAMES = ('CLA', 'CL', 'CL-')

iphasimulator.simulation_gromacs_runner.GROMACS_SOLVATION_TEMPLATE_DIR = 'data/gromacs_solvation'

iphasimulator.simulation_gromacs_runner.GROMACS_SOLVATION_TEMPLATE_NAMES = ('ions.mdp', 'tip3_ions_atomtypes.itp', 'TIP3_SOL.itp', 'TIP3.itp', 'SOD.itp', 'POT.itp', 'CLA.itp')

iphasimulator.simulation_gromacs_runner.GROMACS_SOLVATION_TOPOLOGY_INCLUDE_NAMES = ('tip3_ions_atomtypes.itp', 'TIP3_SOL.itp', 'SOD.itp', 'CLA.itp')

iphasimulator.simulation_gromacs_runner.MINIM_MDP = Multiline-String

Show Value

"""; Energy minimisation
integrator      = steep
emtol           = 1000.0
emstep          = 0.01
nsteps          = 5000
cutoff-scheme   = Verlet
coulombtype     = PME
rcoulomb        = 1.0
rvdw            = 1.0
pbc             = xyz
"""

iphasimulator.simulation_gromacs_runner.NVT_MDP = Multiline-String

Show Value

"""; NVT equilibration
integrator              = md
nsteps                  = 50000
dt                      = 0.002
continuation            = no
constraint_algorithm    = lincs
constraints             = h-bonds
cutoff-scheme           = Verlet
coulombtype             = PME
rcoulomb                = 1.0
rvdw                    = 1.0
tcoupl                  = V-rescale
tc-grps                 = System
tau_t                   = 1.0
ref_t                   = 300
pcoupl                  = no
pbc                     = xyz
gen_vel                 = yes
gen_temp                = 300
gen_seed                = -1
"""

iphasimulator.simulation_gromacs_runner.NPT_MDP = Multiline-String

Show Value

"""; NPT equilibration
integrator              = md
nsteps                  = 50000
dt                      = 0.002
continuation            = yes
constraint_algorithm    = lincs
constraints             = h-bonds
cutoff-scheme           = Verlet
coulombtype             = PME
rcoulomb                = 1.0
rvdw                    = 1.0
tcoupl                  = V-rescale
tc-grps                 = System
tau_t                   = 1.0
ref_t                   = 300
pcoupl                  = C-rescale
pcoupltype              = isotropic
tau_p                   = 5.0
ref_p                   = 1.0
compressibility         = 4.5e-5
pbc                     = xyz
gen_vel                 = no
"""

iphasimulator.simulation_gromacs_runner.PRODUCTION_MDP = Multiline-String

Show Value

"""; Production MD
integrator              = md
nsteps                  = 500000
dt                      = 0.002
continuation            = yes
constraint_algorithm    = lincs
constraints             = h-bonds
cutoff-scheme           = Verlet
coulombtype             = PME
rcoulomb                = 1.0
rvdw                    = 1.0
tcoupl                  = V-rescale
tc-grps                 = System
tau_t                   = 1.0
ref_t                   = 300
pcoupl                  = C-rescale
pcoupltype              = isotropic
tau_p                   = 5.0
ref_p                   = 1.0
compressibility         = 4.5e-5
pbc                     = xyz
gen_vel                 = no
nstxout-compressed      = 1000
nstenergy               = 1000
nstlog                  = 1000
"""

iphasimulator.simulation_gromacs_runner.write_gromacs_run_files(output_dir: str | pathlib.Path, system_name: str = 'system') → GromacsRunFiles: Write basic GROMACS mdp files and a staged run script.

iphasimulator.simulation_gromacs_runner.create_gromacs_simulation_box(input_gro: str | pathlib.Path, output_gro: str | pathlib.Path, *, padding_nm: float = 3.0, box_type: str = 'cubic', gmx_command: str = 'gmx', runner=subprocess.run) → pathlib.Path: Create a centered GROMACS simulation box with gmx editconf.

iphasimulator.simulation_gromacs_runner.validate_gromacs_box_against_mdp(gro_file: str | pathlib.Path, mdp_file: str | pathlib.Path) → GromacsBoxValidation: Warn when a GRO box is too small for the MDP nonbonded cutoffs.

iphasimulator.simulation_gromacs_runner.GROMACS_WORKFLOW_HPC_STEPS

iphasimulator.simulation_gromacs_runner.count_gro_atoms(gro_path: str | pathlib.Path) → int: Read the atom count from the second line of a GROMACS .gro file.

iphasimulator.simulation_gromacs_runner.validate_gromacs_coordinate_topology_counts(output_dir: str | pathlib.Path, *, coordinate_name: str = 'step5_input.gro', topology_name: str = 'topol.top') → GromacsCoordinateTopologyValidation: Compare final coordinate atoms with topology molecule atom counts.

iphasimulator.simulation_gromacs_runner.write_gromacs_solvation_files(output_dir: str | pathlib.Path, *, workflow_type: str = 'polymer', box_padding_nm: float = 1.2, ion_concentration_molar: float = 0.15, clean: bool = False, overwrite: bool = False) → GromacsSolvationFiles

Write files for the standard GROMACS solvate/genion workflow.

This keeps the polymer GAFF2 topology unchanged and only adds the simulation environment: box, TIP3P-compatible water from GROMACS, and neutralising NaCl ions.

iphasimulator.simulation_gromacs_runner.validate_gromacs_solvated_topology(output_dir: str | pathlib.Path, *, topology_name: str = 'topol.top') → GromacsSolvatedTopologyValidation: Validate that topology molecule counts include solvent and ions.

iphasimulator.simulation_gromacs_runner.validate_gromacs_solvation_grompp(output_dir: str | pathlib.Path, *, gmx_command: str = 'gmx', runner=subprocess.run) → tuple[GromacsGromppValidation, GromacsGromppValidation]: Run the two grompp checks required by the solvation workflow.

iphasimulator.simulation_gromacs_runner.validate_gromacs_run_folder(output_dir: str | pathlib.Path, *, topology_name: str = 'topol.top') → GromacsTopologyValidation

Validate external include files referenced by a GROMACS topology.

ParmEd GAFF2 conversion often writes a standalone topology with all molecule definitions in topol.top. In that case there are no #include lines and no toppar directory is required.

iphasimulator.simulation_gromacs_runner.check_gromacs_minimization_inputs(output_dir: str | pathlib.Path) → GromacsLocalMinimizationCheck: Check the files needed before running local GROMACS minimisation.

iphasimulator.simulation_gromacs_runner.run_gromacs_local_minimization(output_dir: str | pathlib.Path, *, runner=subprocess.run) → subprocess.CompletedProcess: Run the local minimisation script from inside the GROMACS folder.

iphasimulator.simulation_gromacs_runner.prepare_gromacs_run_folder(prmtop_file: str | pathlib.Path, inpcrd_file: str | pathlib.Path, output_dir: str | pathlib.Path, system_name: str, *, workflow_type: str = 'polymer', index_file: str | pathlib.Path | None = None, gmx_command: str = 'gmx', runner=subprocess.run) → GromacsPreparedRunFolder

Prepare self-contained GROMACS workflow folders from AMBER files.

output_dir is the system-level gromacs directory. This function writes independent dry_polymer, solvated_polymer and charmm_gui_membrane subdirectories so one workflow cannot overwrite another workflow’s inputs or outputs.

`GROMACS_POLYMER_MDP_TEMPLATE_NAMES`
`GROMACS_CHARMM_GUI_MEMBRANE_MDP_TEMPLATE_NAMES`
`GROMACS_MDP_TEMPLATE_NAMES`
`GROMACS_ALL_MDP_TEMPLATE_NAMES`
`GROMACS_WORKFLOW_MDP_TEMPLATE_NAMES`
`INCLUDE_PATTERN`
`LOCAL_MINIMIZATION_REQUIRED_FILENAMES`
`MDP_CUTOFF_KEYS`
`WATER_MOLECULE_NAMES`
`CATION_MOLECULE_NAMES`
`ANION_MOLECULE_NAMES`
`GROMACS_SOLVATION_TEMPLATE_DIR`
`GROMACS_SOLVATION_TEMPLATE_NAMES`
`GROMACS_SOLVATION_TOPOLOGY_INCLUDE_NAMES`
`MINIM_MDP`
`NVT_MDP`
`NPT_MDP`
`PRODUCTION_MDP`
`GROMACS_WORKFLOW_HPC_STEPS`

iphasimulator.simulation_gromacs_runner

Attributes

Classes

Functions

Module Contents