Simulators

class mdfptools.Simulator.BaseSimulator[source]

Warning

The base class should not be used directly

Parameters

  • temperature (simtk.unit) – default 298.15 K

  • pressure (simtk.unit) – default 1.013 bar

  • time_step (simtk.unit) – default 2 fs

Methods

run(parmed_obj, file_name[, file_path, …])

Runs simulation using OpenMM.

via_gromacs()

Simulation via GROMACS will be added in the future.

via_openmm(parmed_obj, file_name[, …])

Runs simulation using OpenMM.
classmethod via_openmm(parmed_obj, file_name, file_path='./', platform='CUDA', num_steps=2500000, write_out_freq=5000, **kwargs)[source]

Runs simulation using OpenMM.

Parameters

  • parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

  • platform (str) – The computing architecture to do the calculation, default to CUDA, CPU, OpenCL is also possible.

  • num_steps (int) – Number of production simulation to run, default 2,500,000 steps, i.e. 5 ns.

  • write_out_freq (int) – Write out every nth frame of simulated trajectory, default to every 5000 frame write out one, i.e. 10 ps per frame.

Returns

path – The absolute path where the trajectory is written to.

Return type

str

classmethod via_gromacs()[source]

Simulation via GROMACS will be added in the future.

classmethod run(parmed_obj, file_name, file_path='./', platform='CUDA', num_steps=2500000, write_out_freq=5000, **kwargs)

Runs simulation using OpenMM.

Parameters

  • parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

  • platform (str) – The computing architecture to do the calculation, default to CUDA, CPU, OpenCL is also possible.

  • num_steps (int) – Number of production simulation to run, default 2,500,000 steps, i.e. 5 ns.

  • write_out_freq (int) – Write out every nth frame of simulated trajectory, default to every 5000 frame write out one, i.e. 10 ps per frame.

Returns

path – The absolute path where the trajectory is written to.

Return type

str

__init__(self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

class mdfptools.Simulator.SolutionSimulator[source]

Perform solution simulation, namely one copy of solute in water box. Currently identical to BaseSimulator

Parameters

equil_steps (int) – number of steps during equilibraion, default 50,000 steps, i.e. 100 ps

Methods

run(parmed_obj, file_name[, file_path, …])

Runs simulation using OpenMM.

via_gromacs()

Simulation via GROMACS will be added in the future.

via_openmm(parmed_obj, file_name[, …])

Runs simulation using OpenMM.
__init__(self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

classmethod run(parmed_obj, file_name, file_path='./', platform='CUDA', num_steps=2500000, write_out_freq=5000, **kwargs)

Runs simulation using OpenMM.

Parameters

  • parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

  • platform (str) – The computing architecture to do the calculation, default to CUDA, CPU, OpenCL is also possible.

  • num_steps (int) – Number of production simulation to run, default 2,500,000 steps, i.e. 5 ns.

  • write_out_freq (int) – Write out every nth frame of simulated trajectory, default to every 5000 frame write out one, i.e. 10 ps per frame.

Returns

path – The absolute path where the trajectory is written to.

Return type

str

classmethod via_gromacs()

Simulation via GROMACS will be added in the future.

classmethod via_openmm(parmed_obj, file_name, file_path='./', platform='CUDA', num_steps=2500000, write_out_freq=5000, **kwargs)

Runs simulation using OpenMM.

Parameters

  • parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

  • platform (str) – The computing architecture to do the calculation, default to CUDA, CPU, OpenCL is also possible.

  • num_steps (int) – Number of production simulation to run, default 2,500,000 steps, i.e. 5 ns.

  • write_out_freq (int) – Write out every nth frame of simulated trajectory, default to every 5000 frame write out one, i.e. 10 ps per frame.

Returns

path – The absolute path where the trajectory is written to.

Return type

str

class mdfptools.Simulator.LiquidSimulator[source]

Perform liquid simulation, namely multiple copy of the same molecule.

Parameters

equil_steps (int) – number of steps during equilibraion, default 500,000 steps, i.e. 1 ns

Methods

run(parmed_obj, file_name[, file_path, …])

Runs simulation using OpenMM.

via_gromacs()

Simulation via GROMACS will be added in the future.

via_openmm(parmed_obj, file_name[, …])

Runs simulation using OpenMM.
__init__(self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

classmethod run(parmed_obj, file_name, file_path='./', platform='CUDA', num_steps=2500000, write_out_freq=5000, **kwargs)

Runs simulation using OpenMM.

Parameters

  • parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

  • platform (str) – The computing architecture to do the calculation, default to CUDA, CPU, OpenCL is also possible.

  • num_steps (int) – Number of production simulation to run, default 2,500,000 steps, i.e. 5 ns.

  • write_out_freq (int) – Write out every nth frame of simulated trajectory, default to every 5000 frame write out one, i.e. 10 ps per frame.

Returns

path – The absolute path where the trajectory is written to.

Return type

str

classmethod via_gromacs()

Simulation via GROMACS will be added in the future.

classmethod via_openmm(parmed_obj, file_name, file_path='./', platform='CUDA', num_steps=2500000, write_out_freq=5000, **kwargs)

Runs simulation using OpenMM.

Parameters

  • parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

  • platform (str) – The computing architecture to do the calculation, default to CUDA, CPU, OpenCL is also possible.

  • num_steps (int) – Number of production simulation to run, default 2,500,000 steps, i.e. 5 ns.

  • write_out_freq (int) – Write out every nth frame of simulated trajectory, default to every 5000 frame write out one, i.e. 10 ps per frame.

Returns

path – The absolute path where the trajectory is written to.

Return type

str

class mdfptools.Simulator.BaseSimulator[source]

Warning

The base class should not be used directly

Parameters

  • temperature (simtk.unit) – default 298.15 K

  • pressure (simtk.unit) – default 1.013 bar

  • time_step (simtk.unit) – default 2 fs

Methods

run(parmed_obj, file_name[, file_path, …])

Runs simulation using OpenMM.

via_gromacs()

Simulation via GROMACS will be added in the future.

via_openmm(parmed_obj, file_name[, …])

Runs simulation using OpenMM.
classmethod via_openmm(parmed_obj, file_name, file_path='./', platform='CUDA', num_steps=2500000, write_out_freq=5000, **kwargs)[source]

Runs simulation using OpenMM.

Parameters

  • parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

  • platform (str) – The computing architecture to do the calculation, default to CUDA, CPU, OpenCL is also possible.

  • num_steps (int) – Number of production simulation to run, default 2,500,000 steps, i.e. 5 ns.

  • write_out_freq (int) – Write out every nth frame of simulated trajectory, default to every 5000 frame write out one, i.e. 10 ps per frame.

Returns

path – The absolute path where the trajectory is written to.

Return type

str

classmethod via_gromacs()[source]

Simulation via GROMACS will be added in the future.

classmethod run(parmed_obj, file_name, file_path='./', platform='CUDA', num_steps=2500000, write_out_freq=5000, **kwargs)

Runs simulation using OpenMM.

Parameters

  • parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

  • platform (str) – The computing architecture to do the calculation, default to CUDA, CPU, OpenCL is also possible.

  • num_steps (int) – Number of production simulation to run, default 2,500,000 steps, i.e. 5 ns.

  • write_out_freq (int) – Write out every nth frame of simulated trajectory, default to every 5000 frame write out one, i.e. 10 ps per frame.

Returns

path – The absolute path where the trajectory is written to.

Return type

str

__init__(self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

class mdfptools.Simulator.SolutionSimulator[source]

Perform solution simulation, namely one copy of solute in water box. Currently identical to BaseSimulator

Parameters

equil_steps (int) – number of steps during equilibraion, default 50,000 steps, i.e. 100 ps

Methods

run(parmed_obj, file_name[, file_path, …])

Runs simulation using OpenMM.

via_gromacs()

Simulation via GROMACS will be added in the future.

via_openmm(parmed_obj, file_name[, …])

Runs simulation using OpenMM.
__init__(self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

classmethod run(parmed_obj, file_name, file_path='./', platform='CUDA', num_steps=2500000, write_out_freq=5000, **kwargs)

Runs simulation using OpenMM.

Parameters

  • parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

  • platform (str) – The computing architecture to do the calculation, default to CUDA, CPU, OpenCL is also possible.

  • num_steps (int) – Number of production simulation to run, default 2,500,000 steps, i.e. 5 ns.

  • write_out_freq (int) – Write out every nth frame of simulated trajectory, default to every 5000 frame write out one, i.e. 10 ps per frame.

Returns

path – The absolute path where the trajectory is written to.

Return type

str

classmethod via_gromacs()

Simulation via GROMACS will be added in the future.

classmethod via_openmm(parmed_obj, file_name, file_path='./', platform='CUDA', num_steps=2500000, write_out_freq=5000, **kwargs)

Runs simulation using OpenMM.

Parameters

  • parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

  • platform (str) – The computing architecture to do the calculation, default to CUDA, CPU, OpenCL is also possible.

  • num_steps (int) – Number of production simulation to run, default 2,500,000 steps, i.e. 5 ns.

  • write_out_freq (int) – Write out every nth frame of simulated trajectory, default to every 5000 frame write out one, i.e. 10 ps per frame.

Returns

path – The absolute path where the trajectory is written to.

Return type

str

class mdfptools.Simulator.LiquidSimulator[source]

Perform liquid simulation, namely multiple copy of the same molecule.

Parameters

equil_steps (int) – number of steps during equilibraion, default 500,000 steps, i.e. 1 ns

Methods

run(parmed_obj, file_name[, file_path, …])

Runs simulation using OpenMM.

via_gromacs()

Simulation via GROMACS will be added in the future.

via_openmm(parmed_obj, file_name[, …])

Runs simulation using OpenMM.
__init__(self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

classmethod run(parmed_obj, file_name, file_path='./', platform='CUDA', num_steps=2500000, write_out_freq=5000, **kwargs)

Runs simulation using OpenMM.

Parameters

  • parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

  • platform (str) – The computing architecture to do the calculation, default to CUDA, CPU, OpenCL is also possible.

  • num_steps (int) – Number of production simulation to run, default 2,500,000 steps, i.e. 5 ns.

  • write_out_freq (int) – Write out every nth frame of simulated trajectory, default to every 5000 frame write out one, i.e. 10 ps per frame.

Returns

path – The absolute path where the trajectory is written to.

Return type

str

classmethod via_gromacs()

Simulation via GROMACS will be added in the future.

classmethod via_openmm(parmed_obj, file_name, file_path='./', platform='CUDA', num_steps=2500000, write_out_freq=5000, **kwargs)

Runs simulation using OpenMM.

Parameters

  • parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

  • platform (str) – The computing architecture to do the calculation, default to CUDA, CPU, OpenCL is also possible.

  • num_steps (int) – Number of production simulation to run, default 2,500,000 steps, i.e. 5 ns.

  • write_out_freq (int) – Write out every nth frame of simulated trajectory, default to every 5000 frame write out one, i.e. 10 ps per frame.

Returns

path – The absolute path where the trajectory is written to.

Return type

str