iphasimulator.sw_openmm
=======================

.. py:module:: iphasimulator.sw_openmm


Classes
-------

.. autoapisummary::

   iphasimulator.sw_openmm.DcdWriter
   iphasimulator.sw_openmm.DataWriter
   iphasimulator.sw_openmm.BuildSimulation
   iphasimulator.sw_openmm.GromacsSimulation
   iphasimulator.sw_openmm.AmberSimulation


Module Contents
---------------

.. py:class:: DcdWriter(prefix, freq)

   Write DCD trajectory files for OpenMM simulations.


   .. py:attribute:: dcdReporter


.. py:class:: DataWriter(prefix, freq, steps)

   Write OpenMM state data to a comma-separated text file.


   .. py:attribute:: stateDataReporter


.. py:class:: BuildSimulation(manager, filename, output_dir=None)

   Parent class for OpenMM simulations.

   Child classes:

       AmberSimulation

       GromacsSimulation



   .. py:attribute:: savepdb_traj
      :value: False



   .. py:attribute:: pressure
      :value: 1



   .. py:attribute:: temp
      :value: 300



   .. py:attribute:: min_temp
      :value: 0



   .. py:attribute:: timestep
      :value: 2.0



   .. py:attribute:: friction_coeff
      :value: 1.0



   .. py:attribute:: total_steps
      :value: 1000



   .. py:attribute:: reporter_freq
      :value: 1000



   .. py:attribute:: nonbondedcutoff
      :value: 1.0



   .. py:attribute:: timestamp


   .. py:attribute:: anneal_parameters
      :value: [300, 700, 5, 10, 500000]



   .. py:attribute:: minimized_only
      :value: None



   .. py:attribute:: restrain_heavys
      :value: False



   .. py:attribute:: manager


   .. py:attribute:: filename


   .. py:attribute:: run_name


   .. py:method:: type_of_simulation()


   .. py:method:: get_platform(platform_name=None)

      Select the OpenMM platform.

      :param platform_name: Force a platform: "CUDA", "OpenCL", or "CPU".
      :type platform_name: str, optional



   .. py:method:: create_openmm_system(ensemble='NVT', temp=None, pressure=None)


   .. py:method:: create_openmm_simulation(system, integrator, platform)


   .. py:method:: minimize_energy()


   .. py:method:: minimize_energy_help()
      :classmethod:



   .. py:method:: 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)


   .. py:method:: anneal_help()
      :classmethod:



   .. py:method:: basic_NPT(simulation, total_steps=None, temp=None, pressure=None, filename=None, save_restart=False, restart_name=None, verbose=True)


   .. py:method:: basic_NPT_help()
      :classmethod:



   .. py:method:: basic_NVT(simulation, total_steps=None, temp=None, filename=None, save_restart=False, restart_name=None, verbose=True)


   .. py:method:: 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)


   .. py:method:: save_rst(simulation, restart_name=None, overwrite=False)


   .. py:method:: restrain_heavy_atoms(system, topology, positions)


   .. py:method:: display_start_time()
      :classmethod:



   .. py:method:: savepdb_trajectories(boolean)
      :classmethod:



   .. py:method:: set_temperature(temp)
      :classmethod:



   .. py:method:: set_pressure(pressure)
      :classmethod:



   .. py:method:: set_timestep(timestep)
      :classmethod:



   .. py:method:: set_friction_coeff(friction_coeff)
      :classmethod:



   .. py:method:: set_total_steps(total_steps)
      :classmethod:



   .. py:method:: set_reporter_freq(reporter_freq)
      :classmethod:



   .. py:method:: set_nonbondedcutoff(nonbondedcutoff)
      :classmethod:



   .. py:method:: set_anneal_parameters(new_anneal_parameters)
      :classmethod:



   .. py:method:: set_anneal_parameters_help()
      :classmethod:



   .. py:method:: graph_state_data(data_file)
      :staticmethod:



   .. py:method:: graph_state_data_help()
      :classmethod:



.. py:class:: GromacsSimulation(manager, topology_file, coordinates_file, output_dir=None)



   OpenMM simulation using GROMACS topology and coordinate files.



   .. py:attribute:: manager


   .. py:attribute:: filename


   .. py:attribute:: coordinates_file


   .. py:attribute:: topology_file


   .. py:attribute:: gro_coordinates


   .. py:attribute:: gro_topology


.. py:class:: AmberSimulation(manager, topology_file, coordinates_file, output_dir=None)



   OpenMM simulation using AMBER topology and coordinate files.


   .. py:attribute:: manager


   .. py:attribute:: filename


   .. py:attribute:: coordinates_file


   .. py:attribute:: topology_file


   .. py:attribute:: amb_coordinates


   .. py:attribute:: amb_topology