iphasimulator.sw_openmm
Classes
Write DCD trajectory files for OpenMM simulations. |
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Write OpenMM state data to a comma-separated text file. |
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Parent class for OpenMM simulations. |
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OpenMM simulation using GROMACS topology and coordinate files. |
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OpenMM simulation using AMBER topology and coordinate files. |
Module Contents
- class iphasimulator.sw_openmm.DcdWriter(prefix, freq)
Write DCD trajectory files for OpenMM simulations.
- dcdReporter
- class iphasimulator.sw_openmm.DataWriter(prefix, freq, steps)
Write OpenMM state data to a comma-separated text file.
- stateDataReporter
- class iphasimulator.sw_openmm.BuildSimulation(manager, filename, output_dir=None)
Parent class for OpenMM simulations.
Child classes:
AmberSimulation
GromacsSimulation
- savepdb_traj = False
- pressure = 1
- temp = 300
- min_temp = 0
- timestep = 2.0
- friction_coeff = 1.0
- total_steps = 1000
- reporter_freq = 1000
- nonbondedcutoff = 1.0
- timestamp
- anneal_parameters = [300, 700, 5, 10, 500000]
- minimized_only = None
- restrain_heavys = False
- manager
- filename
- run_name
- type_of_simulation()
- get_platform(platform_name=None)
Select the OpenMM platform.
- Parameters:
platform_name (str, optional) – Force a platform: “CUDA”, “OpenCL”, or “CPU”.
- create_openmm_system(ensemble='NVT', temp=None, pressure=None)
- create_openmm_simulation(system, integrator, platform)
- minimize_energy()
- classmethod minimize_energy_help()
- anneal_NVT(simulation, start_temp=None, max_temp=None, cycles=None, quench_rate=None, steps_per_cycle=None, filename=None, save_restart=False, restart_name=None, verbose=True)
- classmethod anneal_help()
- basic_NPT(simulation, total_steps=None, temp=None, pressure=None, filename=None, save_restart=False, restart_name=None, verbose=True)
- classmethod basic_NPT_help()
- basic_NVT(simulation, total_steps=None, temp=None, filename=None, save_restart=False, restart_name=None, verbose=True)
- thermal_ramp(simulation, heating=None, quench_rate=None, ensemble=None, start_temp=None, max_temp=None, total_steps=None, pressure=None, filename=None, save_restart=False, restart_name=None)
- save_rst(simulation, restart_name=None, overwrite=False)
- restrain_heavy_atoms(system, topology, positions)
- classmethod display_start_time()
- classmethod savepdb_trajectories(boolean)
- classmethod set_temperature(temp)
- classmethod set_pressure(pressure)
- classmethod set_timestep(timestep)
- classmethod set_friction_coeff(friction_coeff)
- classmethod set_total_steps(total_steps)
- classmethod set_reporter_freq(reporter_freq)
- classmethod set_nonbondedcutoff(nonbondedcutoff)
- classmethod set_anneal_parameters(new_anneal_parameters)
- classmethod set_anneal_parameters_help()
- static graph_state_data(data_file)
- classmethod graph_state_data_help()