DualAMDIntegrator Class Reference

DualAMDIntegrator implements a dual boost aMD integration algorithm. More...

Inheritance diagram for DualAMDIntegrator:

Public Member Functions
def	__init__
	Create a DualAMDIntegrator. More...
def	getAlphaTotal
	Get the value of alpha for the total energy. More...
def	setAlphaTotal
	Set the value of alpha for the total energy. More...
def	getETotal
	Get the energy threshold E for the total energy. More...
def	setETotal
	Set the energy threshold E for the total energy. More...
def	getAlphaGroup
	Get the value of alpha for the boosted force group. More...
def	setAlphaGroup
	Set the value of alpha for the boosted force group. More...
def	getEGroup
	Get the energy threshold E for the boosted force group. More...
def	setEGroup
	Set the energy threshold E for the boosted force group. More...
def	getEffectiveEnergy
	Given the actual potential energy of the system, return the value of the effective potential. More...

Detailed Description

DualAMDIntegrator implements a dual boost aMD integration algorithm.

This is similar to AMDIntegrator, but two different boosts are applied to the potential: one based on the total energy, and one based on the energy of a single force group (typically representing torsions).

For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007).

Constructor & Destructor Documentation

def __init__	(		self,
			dt,
			group,
			alphaTotal,
			ETotal,
			alphaGroup,
			EGroup
	)

Create a DualAMDIntegrator.

Parameters

dt	(time) The integration time step to use
group	(int) The force group to apply the second boost to
alphaTotal	(energy) The alpha parameter to use for the total energy
ETotal	(energy) The energy cutoff to use for the total energy
alphaGroup	(energy) The alpha parameter to use for the boosted force group
EGroup	(energy) The energy cutoff to use for the boosted force group

References CustomIntegrator.addComputeGlobal(), CustomIntegrator.addComputePerDof(), CustomIntegrator.addConstrainPositions(), CustomIntegrator.addGlobalVariable(), CustomIntegrator.addPerDofVariable(), and CustomIntegrator.addUpdateContextState().

Member Function Documentation

def getAlphaGroup

(

self

)

Get the value of alpha for the boosted force group.

References CustomIntegrator.getGlobalVariable().

Referenced by DualAMDIntegrator.getEffectiveEnergy().

def getAlphaTotal

(

self

)

Get the value of alpha for the total energy.

References CustomIntegrator.getGlobalVariable().

Referenced by DualAMDIntegrator.getEffectiveEnergy().

def getEffectiveEnergy	(		self,
			totalEnergy,
			groupEnergy
	)

Given the actual potential energy of the system, return the value of the effective potential.

Parameters

totalEnergy	(energy): the actual potential energy of the whole system
groupEnergy	(energy): the actual potential energy of the boosted force group

Returns

the value of the effective potential

References AMDForceGroupIntegrator.getAlphaGroup(), DualAMDIntegrator.getAlphaGroup(), DualAMDIntegrator.getAlphaTotal(), AMDForceGroupIntegrator.getEGroup(), DualAMDIntegrator.getEGroup(), and DualAMDIntegrator.getETotal().

def getEGroup

(

self

)

Get the energy threshold E for the boosted force group.

References CustomIntegrator.getGlobalVariable().

Referenced by DualAMDIntegrator.getEffectiveEnergy().

def getETotal

(

self

)

Get the energy threshold E for the total energy.

References CustomIntegrator.getGlobalVariable().

Referenced by DualAMDIntegrator.getEffectiveEnergy().

def setAlphaGroup	(		self,
			alpha
	)

Set the value of alpha for the boosted force group.

References CustomIntegrator.setGlobalVariable().

def setAlphaTotal	(		self,
			alpha
	)

Set the value of alpha for the total energy.

References CustomIntegrator.setGlobalVariable().

def setEGroup	(		self,
			E
	)

Set the energy threshold E for the boosted force group.

References CustomIntegrator.setGlobalVariable().

def setETotal	(		self,
			E
	)

Set the energy threshold E for the total energy.

References CustomIntegrator.setGlobalVariable().

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

• amd.py