CMAPTorsionForce Class Reference

This class implements an interaction between pairs of dihedral angles. More...

Inheritance diagram for CMAPTorsionForce:

Public Member Functions
def	getNumMaps
	getNumMaps(CMAPTorsionForce self) -> int More...
def	getNumTorsions
	getNumTorsions(CMAPTorsionForce self) -> int More...
def	addMap
	addMap(CMAPTorsionForce self, int size, vectord energy) -> int More...
def	getMapParameters
	getMapParameters(CMAPTorsionForce self, int index) More...
def	setMapParameters
	setMapParameters(CMAPTorsionForce self, int index, int size, vectord energy) More...
def	addTorsion
	addTorsion(CMAPTorsionForce self, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4) -> int More...
def	getTorsionParameters
	getTorsionParameters(CMAPTorsionForce self, int index) More...
def	setTorsionParameters
	setTorsionParameters(CMAPTorsionForce self, int index, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4) More...
def	__init__
	init(OpenMM::CMAPTorsionForce self) -> CMAPTorsionForce init(OpenMM::CMAPTorsionForce self, CMAPTorsionForce other) -> CMAPTorsionForce More...
def	__del__
	del(OpenMM::CMAPTorsionForce self) More...
Public Member Functions inherited from Force
def	__init__
def	__del__
	del(OpenMM::Force self) More...
def	getForceGroup
	getForceGroup(Force self) -> int More...
def	setForceGroup
	setForceGroup(Force self, int group) More...
def	__copy__
def	__deepcopy__

Public Attributes
	this

Detailed Description

This class implements an interaction between pairs of dihedral angles.

The interaction energy is defined by an "energy correction map" (CMAP), which is simply a set of tabulated energy values on a regular grid of (phi, psi) angles. Natural cubic spline interpolation is used to compute forces and energies at arbitrary values of the two angles.

To use this class, first create one or more energy correction maps by calling addMap(). For each one, you provide an array of energies at uniformly spaced values of the two angles. Next, add interactions by calling addTorsion(). For each one, you specify the sequence of particles used to calculate each of the two dihedral angles, and the index of the map used to calculate their interaction energy.

Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

init(OpenMM::CMAPTorsionForce self) -> CMAPTorsionForce init(OpenMM::CMAPTorsionForce self, CMAPTorsionForce other) -> CMAPTorsionForce

Create a CMAPTorsionForce.

References simtk.openmm.openmm.stripUnits().

def __del__

(

self

)

del(OpenMM::CMAPTorsionForce self)

References simtk.openmm.openmm.stripUnits().

Member Function Documentation

def addMap	(		self,
			args
	)

addMap(CMAPTorsionForce self, int size, vectord energy) -> int

Create a new map that can be used for torsion pairs.

Parameters

size	the size of the map along each dimension
energy	the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.

References simtk.openmm.openmm.stripUnits().

def addTorsion	(		self,
			args
	)

addTorsion(CMAPTorsionForce self, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4) -> int

Add a CMAP torsion term to the force field.

Parameters

map	the index of the map to use for this term
a1	the index of the first particle forming the first torsion
a2	the index of the second particle forming the first torsion
a3	the index of the third particle forming the first torsion
a4	the index of the fourth particle forming the first torsion
b1	the index of the first particle forming the second torsion
b2	the index of the second particle forming the second torsion
b3	the index of the third particle forming the second torsion
b4	the index of the fourth particle forming the second torsion

References simtk.openmm.openmm.stripUnits().

def getMapParameters	(		self,
			args
	)

getMapParameters(CMAPTorsionForce self, int index)

Get the energy values of a map.

Parameters

index	the index of the map for which to get energy values
size	the size of the map along each dimension
energy	the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.

References simtk.openmm.openmm.stripUnits().

def getNumMaps

(

self

)

getNumMaps(CMAPTorsionForce self) -> int

Get the number of maps that have been defined.

References simtk.openmm.openmm.stripUnits().

def getNumTorsions

(

self

)

getNumTorsions(CMAPTorsionForce self) -> int

Get the number of CMAP torsion terms in the potential function

References simtk.openmm.openmm.stripUnits().

def getTorsionParameters	(		self,
			args
	)

getTorsionParameters(CMAPTorsionForce self, int index)

Get the force field parameters for a CMAP torsion term.

Parameters

index	the index of the torsion for which to get parameters
map	the index of the map to use for this term
a1	the index of the first particle forming the first torsion
a2	the index of the second particle forming the first torsion
a3	the index of the third particle forming the first torsion
a4	the index of the fourth particle forming the first torsion
b1	the index of the first particle forming the second torsion
b2	the index of the second particle forming the second torsion
b3	the index of the third particle forming the second torsion
b4	the index of the fourth particle forming the second torsion

References simtk.openmm.openmm.stripUnits().

def setMapParameters	(		self,
			args
	)

setMapParameters(CMAPTorsionForce self, int index, int size, vectord energy)

Set the energy values of a map.

Parameters

index	the index of the map for which to set energy values
size	the size of the map along each dimension
energy	the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.

References simtk.openmm.openmm.stripUnits().

def setTorsionParameters	(		self,
			args
	)

setTorsionParameters(CMAPTorsionForce self, int index, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4)

Set the force field parameters for a CMAP torsion term.

Parameters

index	the index of the torsion for which to set parameters
map	the index of the map to use for this term
a1	the index of the first particle forming the first torsion
a2	the index of the second particle forming the first torsion
a3	the index of the third particle forming the first torsion
a4	the index of the fourth particle forming the first torsion
b1	the index of the first particle forming the second torsion
b2	the index of the second particle forming the second torsion
b3	the index of the third particle forming the second torsion
b4	the index of the fourth particle forming the second torsion

References simtk.openmm.openmm.stripUnits().

Member Data Documentation

this

Referenced by System.__init__().

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

• openmm.py