CLI Usage¶

gbsa-pipeline provides a single command that runs the full GBSA MD simulation pipeline from a TOML configuration file.

Installation¶

The package is installed via Pixi:

pixi install -e dev

After installation the gbsa-pipeline executable is available inside the Pixi environment.

Running a simulation¶

gbsa-pipeline config.toml

Optionally specify an output directory:

gbsa-pipeline config.toml -o results/my_run

Enable verbose (debug) logging:

gbsa-pipeline config.toml -v

Minimal configuration¶

Create a file called config.toml alongside your input files:

[system]
protein = "protein.pdb"
ligand  = "ligand.sdf"

[solvation]
water_model = "tip3p"
padding = 10.0

[md]
nsteps = 500000
dt     = 0.002

All sections except [system] are optional and fall back to sensible defaults. See Configuration Reference for all available fields.

Output structure¶

Running the pipeline creates a numbered directory for each stage under the output directory (default: gbsa_output/ next to the config file):

Directory	Contents
`01_parametrize/`	GROMACS `.gro` and `.top` after force-field assignment
`02_solvated.gro` / `.top`	Solvated system with water box and counter-ions
`03_minimized.gro` / `.top`	Energy-minimized coordinates
`04_equilibrated.gro` / `.top`	NVT-heated (0 → 300 K) coordinates
`05_production.gro` / `.top`	Final production MD coordinates
`run_config.json`	Snapshot of the resolved configuration (for reproducibility)

Full NPT example¶

[system]
protein   = "apo_protein.pdb"
ligand    = "inhibitor.sdf"
net_charge = -1

[forcefield]
protein_ff    = "ff14SB"
ligand_ff     = "gaff2"
charge_method = "am1bcc"

[solvation]
water_model      = "tip3p"
box_shape        = "truncated_octahedron"
padding          = 12.0
ion_concentration = 0.15
neutralize       = true

[minimization]
nsteps = 5000
emtol  = 10.0

[equilibration]
simulation_time_ps = 500.0

[md]
integrator    = "md"
nsteps        = 2500000   # 5 ns at dt=0.002
dt            = 0.002
tcoupl        = "v-rescale"
ref_t         = 300.0
tau_t         = 0.1
pcoupl        = "Parrinello-Rahman"
ref_p         = 1.0
tau_p         = 2.0
compressibility = 4.5e-5
constraints   = "h-bonds"