System

class OpenMM::System

This class represents a molecular system. The definition of a System involves four elements:

• The set of particles in the system

• The forces acting on them

• Pairs of particles whose separation should be constrained to a fixed value

• For periodic systems, the dimensions of the periodic box

The particles and constraints are defined directly by the System object, while forces are defined by objects that extend the Force class. After creating a System, call addParticle() once for each particle, addConstraint() for each constraint, and addForce() for each Force.

In addition, particles may be designated as “virtual sites”. These are particles whose positions are computed automatically based on the positions of other particles. To define a virtual site, call setVirtualSite(), passing in a VirtualSite object that defines the rules for computing its position.

Methods

System	Create a new System.
~System
getNumParticles	Get the number of particles in this System.
addParticle	Add a particle to the System.
getParticleMass	Get the mass (in atomic mass units) of a particle.
setParticleMass	Set the mass (in atomic mass units) of a particle.
setVirtualSite	Set a particle to be a virtual site.
isVirtualSite	Get whether a particle is a VirtualSite.
getVirtualSite	Get VirtualSite object for a particle.
getNumConstraints	Get the number of distance constraints in this System.
addConstraint	Add a constraint to the System.
getConstraintParameters	Get the parameters defining a distance constraint.
setConstraintParameters	Set the parameters defining a distance constraint.
removeConstraint	Remove a constraint from the System.
addForce	Add a Force to the System.
getNumForces	Get the number of Force objects that have been added to the System.
getForce	Get a const reference to one of the Forces in this System.
getForce	Get a writable reference to one of the Forces in this System.
removeForce	Remove a Force from the System.
getDefaultPeriodicBoxVectors	Get the default values of the vectors defining the axes of the periodic box (measured in nm).
setDefaultPeriodicBoxVectors	Set the default values of the vectors defining the axes of the periodic box (measured in nm).
usesPeriodicBoundaryConditions	Returns whether or not any forces in this System use periodic boundaries.

System()

Create a new System().

~System()

int getNumParticles() const

Get the number of particles in this System.

int addParticle(double mass)

Add a particle to the System. If the mass is 0, Integrators will ignore the particle and not modify its position or velocity. This is most often used for virtual sites, but can also be used as a way to prevent a particle from moving.

Parameters

• mass – the mass of the particle (in atomic mass units)

Returns

the index of the particle that was added

double getParticleMass(int index) const

Get the mass (in atomic mass units) of a particle. If the mass is 0, Integrators will ignore the particle and not modify its position or velocity. This is most often used for virtual sites, but can also be used as a way to prevent a particle from moving.

Parameters

• index – the index of the particle for which to get the mass

void setParticleMass(int index, double mass)

Set the mass (in atomic mass units) of a particle. If the mass is 0, Integrators will ignore the particle and not modify its position or velocity. This is most often used for virtual sites, but can also be used as a way to prevent a particle from moving.

Parameters

• index – the index of the particle for which to set the mass

• mass – the mass of the particle

void setVirtualSite(int index, VirtualSite *virtualSite)

Set a particle to be a virtual site. The VirtualSite object should have been created on the heap with the “new” operator. The System takes over ownership of it, and deletes it when the System itself is deleted.

Parameters

• index – the index of the particle that should be treated as a virtual site

• virtualSite – a pointer to the VirtualSite object describing it

bool isVirtualSite(int index) const

Get whether a particle is a VirtualSite.

Parameters

• index – the index of the particle to check

const VirtualSite &getVirtualSite(int index) const

Get VirtualSite object for a particle. If the particle is not a virtual site, this throws an exception.

Parameters

• index – the index of the particle to get

int getNumConstraints() const

Get the number of distance constraints in this System.

int addConstraint(int particle1, int particle2, double distance)

Add a constraint to the System. Particles whose mass is 0 cannot participate in constraints.

Parameters

• particle1 – the index of the first particle involved in the constraint

• particle2 – the index of the second particle involved in the constraint

• distance – the required distance between the two particles, measured in nm

Returns

the index of the constraint that was added

void getConstraintParameters(int index, int &particle1, int &particle2, double &distance) const

Get the parameters defining a distance constraint.

Parameters

• index – the index of the constraint for which to get parameters

• particle1 – [out] the index of the first particle involved in the constraint

• particle2 – [out] the index of the second particle involved in the constraint

• distance – [out] the required distance between the two particles, measured in nm

void setConstraintParameters(int index, int particle1, int particle2, double distance)

Set the parameters defining a distance constraint. Particles whose mass is 0 cannot participate in constraints.

Parameters

• index – the index of the constraint for which to set parameters

• particle1 – the index of the first particle involved in the constraint

• particle2 – the index of the second particle involved in the constraint

• distance – the required distance between the two particles, measured in nm

void removeConstraint(int index)

Remove a constraint from the System.

Parameters

• index – the index of the constraint to remove

int addForce(Force *force)

Add a Force to the System. The Force should have been created on the heap with the “new” operator. The System takes over ownership of it, and deletes the Force when the System itself is deleted.

Parameters

• force – a pointer to the Force object to be added

Returns

the index within the System of the Force that was added

int getNumForces() const

Get the number of Force objects that have been added to the System.

const Force &getForce(int index) const

Get a const reference to one of the Forces in this System.

Parameters

• index – the index of the Force to get

Force &getForce(int index)

Get a writable reference to one of the Forces in this System.

Parameters

• index – the index of the Force to get

void removeForce(int index)

Remove a Force from the System. The memory associated with the removed Force object is deleted.

Parameters

• index – the index of the Force to remove

void getDefaultPeriodicBoxVectors(Vec3 &a, Vec3 &b, Vec3 &c) const

Get the default values of the vectors defining the axes of the periodic box (measured in nm). Any newly created Context will have its box vectors set to these. They will affect any Force added to the System that uses periodic boundary conditions.

Parameters

• a – [out] the vector defining the first edge of the periodic box

• b – [out] the vector defining the second edge of the periodic box

• c – [out] the vector defining the third edge of the periodic box

void setDefaultPeriodicBoxVectors(const Vec3 &a, const Vec3 &b, const Vec3 &c)

Set the default values of the vectors defining the axes of the periodic box (measured in nm). Any newly created Context will have its box vectors set to these. They will affect any Force added to the System that uses periodic boundary conditions.

Triclinic boxes are supported, but the vectors must satisfy certain requirements. In particular, a must point in the x direction, b must point “mostly” in the y direction, and c must point “mostly” in the z direction. See the documentation for details.

Parameters

• a – the vector defining the first edge of the periodic box

• b – the vector defining the second edge of the periodic box

• c – the vector defining the third edge of the periodic box

bool usesPeriodicBoundaryConditions() const

Returns whether or not any forces in this System use periodic boundaries.

If a force in this System does not implement usesPeriodicBoundaryConditions a OpenMM::OpenMMException is thrown

Returns

true if at least one force uses PBC and false otherwise