IMP.pmi.samplers.MolecularDynamics Class Reference

Sample using molecular dynamics. More...

Inherits _SamplerBase.

Detailed Description

Sample using molecular dynamics.

Note

This class is only available in Python.

Definition at line 256 of file samplers.py.

Public Member Functions
def	__init__
	Setup MD. More...
def	set_use_jax
	Request that sampling of the scoring function is done using JAX instead of IMP's internal C++ implementation (requires that all PMI restraints used have a JAX implementation). More...

Constructor & Destructor Documentation

def IMP.pmi.samplers.MolecularDynamics.__init__	(		self,
			model,
			objects,
			kt,
			gamma = 0.01,
			maximum_time_step = 1.0,
			sf = None,
			use_jax = False,
			start_frame = 0
	)

Setup MD.

Parameters

model	The IMP Model
objects	What to sample. Use flat list of particles
kt	Temperature
gamma	Viscosity parameter
maximum_time_step	MD max time step
start_frame	The starting frame number

Definition at line 264 of file samplers.py.

Member Function Documentation

def IMP.pmi.samplers.MolecularDynamics.set_use_jax	(		self,
			nstep
	)

Request that sampling of the scoring function is done using JAX instead of IMP's internal C++ implementation (requires that all PMI restraints used have a JAX implementation).

Definition at line 289 of file samplers.py.

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The documentation for this class was generated from the following file:

• samplers.py