cgexplore.utilities.run_soft_md_cycle

cgexplore.utilities.run_soft_md_cycle(name, assigned_system, output_dir, num_steps, suffix, bond_ff_scale, angle_ff_scale, temperature, time_step, friction, reporting_freq, traj_freq, platform)[source]

Run MD exploration with soft potentials.

Parameters:

  • name (str) – Name to use for naming output files. E.g. produces a file {name}_opted1.mol in output_dir.

  • assigned_system (AssignedSystem) – The system to optimise with force field assigned.

  • output_dir (Path) – Directory to save outputs of optimisation process.

  • num_steps (int) – The number of time steps to run the MD for.

  • suffix (str) – Suffix to use for naming output files. E.g. produces a file {name}_{suffix}_ff.xml in output_dir. Used to define step in process.

  • bond_ff_scale (float) – Scale (divide) the bond terms in the model by this value.

  • angle_ff_scale (float) – Scale (divide) the angle terms in the model by this value.

  • temperature (Quantity) – Simulation temperature. Should be an openmm.unit.Quantity with units of openmm.unit.kelvin.

  • time_step (Quantity) – Simulation timestep to use in Integrator. Should be an openmm.unit.Quantity with units of [time], e.g., openmm.unit.femtoseconds.

  • friction (Quantity) – Friction constant to use in LangevinIntegrator. Should be an openmm.unit.Quantity with units of [time^-1], e.g., / openmm.unit.picosecond.

  • reporting_freq (float) – How often the simulation properties should be written in time steps.

  • traj_freq (float) – How often the trajectory should be written in time steps.

  • platform (str | None) – Which platform to use with OpenMM optimisation. Options are CPU or CUDA. More are available but may not work well out of the box.

Returns:

An OMMTrajectory containing the data and conformers.

Return type:

OMMTrajectory | None