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 theForce
class. After creating aSystem
, calladdParticle()
once for each particle,addConstraint()
for each constraint, andaddForce()
for eachForce
.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 aVirtualSite
object that defines the rules for computing its position.Methods
Create a new
System
.Get the number of particles in this
System
.Add a particle to the
System
.Get the mass (in atomic mass units) of a particle.
Set the mass (in atomic mass units) of a particle.
Set a particle to be a virtual site.
Get whether a particle is a
VirtualSite
.Get
VirtualSite
object for a particle.Get the number of distance constraints in this
System
.Add a constraint to the
System
.Get the parameters defining a distance constraint.
Set the parameters defining a distance constraint.
Remove a constraint from the
System
.Get the number of
Force
objects that have been added to theSystem
.Get a const reference to one of the Forces in this
System
.Get a writable reference to one of the Forces in this
System
.Get the default values of the vectors defining the axes of the periodic box (measured in nm).
Set the default values of the vectors defining the axes of the periodic box (measured in nm).
Returns whether or not any forces in this
System
use periodic boundaries.-
~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. TheSystem
takes over ownership of it, and deletes it when theSystem
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
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 theSystem
. TheForce
should have been created on the heap with the “new” operator. TheSystem
takes over ownership of it, and deletes theForce
when theSystem
itself is deleted.- Parameters
force – a pointer to the
Force
object to be added
-
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 theSystem
. The memory associated with the removedForce
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 anyForce
added to theSystem
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 anyForce
added to theSystem
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 aOpenMM::OpenMMException
is thrown- Returns
true if at least one force uses PBC and false otherwise