RMSDForce

class simtk.openmm.openmm.RMSDForce(*args)

This is a force whose energy equals the root mean squared deviation (RMSD) between the current coordinates and a reference structure. It is intended for use with CustomCVForce. You will not normally want a force that exactly equals the RMSD, but there are many situations where it is useful to have a restraining or biasing force that depends on the RMSD in some way.

The force is computed by first aligning the particle positions to the reference structure, then computing the RMSD between the aligned positions and the reference. The computation can optionally be done based on only a subset of the particles in the system.

__init__(self, referencePositions, particles) → RMSDForce

__init__(self, referencePositions) -> RMSDForce __init__(self, other) -> RMSDForce

Create an RMSDForce.

Parameters:
  • referencePositions (vector< Vec3 >) – the reference positions to compute the deviation from. The length of this vector must equal the number of particles in the system, even if not all particles are used in computing the RMSD.
  • particles (vector< int >) – the indices of the particles to use when computing the RMSD. If this is empty (the default), all particles in the system will be used.

Methods

__init__((self, referencePositions, ...) __init__(self, referencePositions) -> RMSDForce
getForceGroup((self) -> int) Get the force group this Force belongs to.
getParticles((self) -> vectori) Get the indices of the particles to use when computing the RMSD.
getReferencePositions(...) Get the reference positions to compute the deviation from.
setForceGroup(self, group) Set the force group this Force belongs to.
setParticles(self, particles) Set the indices of the particles to use when computing the RMSD.
setReferencePositions(self, positions) Set the reference positions to compute the deviation from.
updateParametersInContext(self, context) Update the reference positions and particle indices in a Context to match those stored in this Force object.
usesPeriodicBoundaryConditions((self) -> bool) Returns whether or not this force makes use of periodic boundary conditions.
getReferencePositions(self) → std::vector< Vec3,std::allocator< Vec3 > > const &

Get the reference positions to compute the deviation from.

setReferencePositions(self, positions)

Set the reference positions to compute the deviation from.

getParticles(self) → vectori

Get the indices of the particles to use when computing the RMSD. If this is empty, all particles in the system will be used.

setParticles(self, particles)

Set the indices of the particles to use when computing the RMSD. If this is empty, all particles in the system will be used.

updateParametersInContext(self, context)

Update the reference positions and particle indices 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 setReferencePositions() and setParticles() to modify this object’s parameters, then call updateParametersInContext() to copy them over to the Context.

usesPeriodicBoundaryConditions(self) → bool

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

Returns:true if force uses PBC and false otherwise
Return type:bool
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__sizeof__() → int

size of object in memory, in bytes

__str__
getForceGroup(self) → int

Get the force group this Force belongs to.

setForceGroup(self, group)

Set the force group this Force belongs to.

Parameters:group (int) – the group index. Legal values are between 0 and 31 (inclusive).