AmoebaBondForce Class Reference

This class implements an interaction between pairs of particles that varies with the distance between them. More...

Inheritance diagram for AmoebaBondForce:

List of all members.

Public Member Functions
def	getNumBonds
	getNumBonds(self) -> int
def	setAmoebaGlobalBondCubic
	Set the global cubic term.
def	getAmoebaGlobalBondCubic
	getAmoebaGlobalBondCubic(self) -> double
def	setAmoebaGlobalBondQuartic
	Set the global quartic term.
def	getAmoebaGlobalBondQuartic
	getAmoebaGlobalBondQuartic(self) -> double
def	addBond
	addBond(self, particle1, particle2, length, quadraticK) -> int
def	getBondParameters
	Get the force field parameters for a bond term.
def	setBondParameters
	Set the force field parameters for a bond term.
def	updateParametersInContext
	Update the per-bond parameters in a Context to match those stored in this Force object.
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(self) -> bool
def	__init__
	__init__(self) -> AmoebaBondForce __init__(self, other) -> AmoebaBondForce
Public Attributes
	this

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Detailed Description

This class implements an interaction between pairs of particles that varies with the distance between them.

The interaction is defined by a 4th order polynomial. Only the quadratic term is set per-bond. The coefficients of the higher order terms each have a single value that is set globally.

To use it, create an AmoebaBondForce object then call addBond() once for each bond. After a bond has been added, you can modify its force field parameters by calling setBondParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

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Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

__init__(self) -> AmoebaBondForce __init__(self, other) -> AmoebaBondForce

Create an AmoebaBondForce.

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Member Function Documentation

def addBond	(		self,
			particle1,
			particle2,
			length,
			quadraticK
	)

addBond(self, particle1, particle2, length, quadraticK) -> int

Add a bond term to the force field.

Parameters:

particle1	(int) the index of the first particle connected by the bond
particle2	(int) the index of the second particle connected by the bond
length	(double) the equilibrium length of the bond, measured in nm
quadraticK	(double) the quadratic force constant for the bond

Returns:

(int) the index of the bond that was added

def getAmoebaGlobalBondCubic

(

self

)

getAmoebaGlobalBondCubic(self) -> double

Get the global cubic term

Returns:

(double) global cubicK term

def getAmoebaGlobalBondQuartic

(

self

)

getAmoebaGlobalBondQuartic(self) -> double

Get the global quartic term

Returns:

(double) global quartic term

def getBondParameters	(		self,
			index
	)

Get the force field parameters for a bond term.

Parameters:

index

(int) the index of the bond for which to get parameters

Returns:

(int) the index of the first particle connected by the bond

(int) the index of the second particle connected by the bond

(double) the equilibrium length of the bond, measured in nm

(double) the quadratic force constant for the bond

def getNumBonds

(

self

)

getNumBonds(self) -> int

Get the number of bond stretch terms in the potential function

def setAmoebaGlobalBondCubic	(		self,
			cubicK
	)

Set the global cubic term.

Parameters:

cubicK

(double) the cubic force constant for the bond

def setAmoebaGlobalBondQuartic	(		self,
			quarticK
	)

Set the global quartic term.

Parameters:

quarticK

(double) the quartic force constant for the bond

def setBondParameters	(		self,
			index,
			particle1,
			particle2,
			length,
			quadraticK
	)

Set the force field parameters for a bond term.

Parameters:

index	(int) the index of the bond for which to set parameters
particle1	(int) the index of the first particle connected by the bond
particle2	(int) the index of the second particle connected by the bond
length	(double) the equilibrium length of the bond, measured in nm
quadraticK	(double) the quadratic force constant for the bond

def updateParametersInContext	(		self,
			context
	)

Update the per-bond parameters in a Context to match those stored in this Force object.

This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call setBondParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.

The only information this method updates is the values of per-bond parameters. The set of particles involved in a bond cannot be changed, nor can new bonds be added.

def usesPeriodicBoundaryConditions

(

self

)

usesPeriodicBoundaryConditions(self) -> bool

Returns whether or not this force makes use of periodic boundary conditions.

Returns:

(bool) true if nonbondedMethod uses PBC and false otherwise

Reimplemented from Force.

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Member Data Documentation

this

Reimplemented from Force.

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

• openmm.py