openmm_utils
OpenMM simulation utilities for box compression and equilibration.
funcmonitor_volume_convergence(volumes, window_size=10, tolerance=0.02)Check if box volume has converged by comparing running averages.
paramvolumeslist of floatVolume values recorded at each reporting interval.
paramwindow_sizeint= 10Number of steps for each running-average window. Default is 10.
paramtolerancefloat= 0.02Relative tolerance for convergence (e.g. 0.02 = 2%). Default is 0.02.
Returns
boolWhether the relative change between consecutive windows is below tolerance.
funcsimulate_compression_until_constant_volume(simulation, steps=100000, tolerance=0.05) → tuple[list[float], int, bool]Run an NPT simulation until the box volume converges.
Step the simulation forward in 1000-step increments, recording the volume
after each increment, and stop early when monitor_volume_convergence
signals convergence.
paramsimulationopenmm.app.SimulationAn initialized OpenMM simulation with a barostat.
paramstepsint= 100000Maximum number of MD steps. Default is 100000.
paramtolerancefloat= 0.05Relative volume-change tolerance passed to
monitor_volume_convergence. Default is 0.05.
Returns
list of floatRecorded box volumes in nm^3.
funcsimulate_compression_until_density_reached(simulation, mass, steps=100000, target_density=1.0) → tuple[list[float], int, bool]Run an NPT simulation until the system density reaches a target value.
Step the simulation in 1000-step increments and compute the instantaneous density from the total mass and current box volume. Stop early once the density meets or exceeds target_density.
paramsimulationopenmm.app.SimulationAn initialized OpenMM simulation with a barostat.
parammassopenmm.unit.QuantityTotal mass of the system (with OpenMM units attached).
paramstepsint= 100000Maximum number of MD steps. Default is 100000.
paramtarget_densityfloat= 1.0Target density in g/mL. Default is 1.0.
Returns
list of floatRecorded densities in g/mL at each reporting interval.
funccreate_sphere(u, pdb, top, radius, steps=100000)Compress a system into a sphere using a harmonic radial restraint.
Apply a custom external force that penalizes atoms beyond radius from the origin, minimize, and run Langevin dynamics to pack the system into a spherical shape.
paramumda.UniverseReference MDAnalysis Universe whose topology is preserved in the returned object.
parampdbstr or PathPath to the input PDB file for OpenMM.
paramtopstr or PathPath to the GROMACS topology file.
paramradiusfloatSphere radius in nanometers.
paramstepsint= 100000Number of MD steps to run after minimization. Default is 100000.
Returns
MDAnalysis.UniverseUniverse with updated positions packed into the sphere. Box dimensions are set to None (non-periodic).
funccompress_box(u, pdb, top, target_density=1.0, pressure=1000.0, steps_compression=200000)Compress a periodic box to a target density using high-pressure NPT.
Apply a Monte Carlo barostat at elevated pressure, minimize, and run dynamics until the system density reaches target_density.
paramumda.UniverseReference MDAnalysis Universe whose topology is preserved in the returned object.
parampdbstr or PathPath to the input PDB file for OpenMM.
paramtopstr or PathPath to the GROMACS topology file.
paramtarget_densityfloat= 1.0Target density in g/mL. Default is 1.0.
parampressurefloat= 1000.0Barostat pressure in bar. Default is 1000.0.
paramsteps_compressionint= 200000Maximum number of compression MD steps. Default is 200000.
Returns
MDAnalysis.UniverseUniverse with compressed positions and updated box dimensions. Positions are wrapped by residue.
funccompress_equilibrate_bilayer(u, pdb, top, pressure=1000.0, steps_compression=200000, steps_equil=0)Compress and equilibrate a lipid bilayer in two phases.
Phase 1 applies z-coordinate restraints with a membrane barostat at elevated pressure (XY-isotropic, Z-fixed) until volume converges. Phase 2 removes the restraints and continues equilibration at 1 bar.
paramumda.UniverseReference MDAnalysis Universe whose topology is preserved in the returned object.
parampdbstr or PathPath to the input PDB file for OpenMM.
paramtopstr or PathPath to the GROMACS topology file.
parampressurefloat= 1000.0Barostat pressure in bar for Phase 1. Default is 1000.0.
paramsteps_compressionint= 200000Maximum MD steps for Phase 1 compression. Default is 200000.
paramsteps_equilint= 0Maximum MD steps for Phase 2 equilibration. Default is 0.
Returns
MDAnalysis.UniverseEquilibrated bilayer Universe with updated positions and box
dimensions. An equilibration_analysis.png plot is also saved.