Package ffx.openmm

Class System

java.lang.Object
ffx.openmm.System
Direct Known Subclasses:
OpenMMSystem
public class System extends Object
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.

  • Constructor Details

    • System

      public System()
      Constructor.

    • System

      public System(com.sun.jna.ptr.PointerByReference pointer)
      Constructor.
      Parameters:
      pointer - The OpenMM System pointer.

  • Method Details

    • addConstraint

      public int addConstraint(int particle1, int particle2, double distance)
      Add a constraint to the system.
      Parameters:
      particle1 - The first particle.
      particle2 - The second particle.
      distance - The distance between the particles.
      Returns:
      The index of the constraint that was added.

    • addForce

      public int addForce(Force force)
      Add a force to the system.
      Parameters:
      force - The force to add.
      Returns:
      The index of the force that was added.

    • addParticle

      public 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

    • destroy

      public void destroy()
      Destroy the system.

    • getConstraintParameters

      public void getConstraintParameters(int index, com.sun.jna.ptr.IntByReference particle1, com.sun.jna.ptr.IntByReference particle2, com.sun.jna.ptr.DoubleByReference distance)
      Get the parameters defining a constraint.
      Parameters:
      index - The index of the constraint.
      particle1 - The index of the first particle involved in the constraint (output).
      particle2 - The index of the second particle involved in the constraint (output).
      distance - The required distance between the two particles (output).

    • getConstraintParameters

      public void getConstraintParameters(int index, IntBuffer particle1, IntBuffer particle2, DoubleBuffer distance)
      Get the parameters defining a constraint.
      Parameters:
      index - The index of the constraint.
      particle1 - The index of the first particle involved in the constraint (output).
      particle2 - The index of the second particle involved in the constraint (output).
      distance - The required distance between the two particles (output).

    • getDefaultPeriodicBoxVectors

      public void getDefaultPeriodicBoxVectors(edu.uiowa.jopenmm.OpenMM_Vec3 a, edu.uiowa.jopenmm.OpenMM_Vec3 b, edu.uiowa.jopenmm.OpenMM_Vec3 c)
      Get the default periodic box vectors.
      Parameters:
      a - The first vector (output).
      b - The second vector (output).
      c - The third vector (output).

    • getForce

      public Force getForce(int index)
      Get a force in the system.
      Parameters:
      index - The index of the force to get.
      Returns:
      The force object.

    • getNumConstraints

      public int getNumConstraints()
      Get the number of constraints in the system.
      Returns:
      The number of constraints in the system.

    • getNumForces

      public int getNumForces()
      Get the number of forces in the system.
      Returns:
      The number of forces in the system.

    • getNumParticles

      public int getNumParticles()
      Get the number of particles in the system.
      Returns:
      The number of particles in the system.

    • getParticleMass

      public double getParticleMass(int index)
      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
      Returns:
      the mass of the particle (in atomic mass units)

    • getPointer

      public com.sun.jna.ptr.PointerByReference getPointer()
      Get the pointer to the system.
      Returns:
      The pointer to the system.

    • getVirtualSite

      public VirtualSite getVirtualSite(int index)
      Get the virtual site for a particle.
      Parameters:
      index - The index of the particle.
      Returns:
      The virtual site object.

    • isVirtualSite

      public boolean isVirtualSite(int index)
      Check if a particle is a virtual site.
      Parameters:
      index - The index of the particle.
      Returns:
      True if the particle is a virtual site.

    • removeConstraint

      public void removeConstraint(int index)
      Remove a constraint from the system.
      Parameters:
      index - The index of the constraint to remove.

    • removeForce

      public void removeForce(int index)
      Remove a force from the system.
      Parameters:
      index - The index of the force to remove.

    • setConstraintParameters

      public void setConstraintParameters(int index, int particle1, int particle2, double distance)
      Set the parameters defining a constraint.
      Parameters:
      index - The index of the constraint.
      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.

    • setDefaultPeriodicBoxVectors

      public void setDefaultPeriodicBoxVectors(edu.uiowa.jopenmm.OpenMM_Vec3 a, edu.uiowa.jopenmm.OpenMM_Vec3 b, edu.uiowa.jopenmm.OpenMM_Vec3 c)
      Set the default periodic box vectors.
      Parameters:
      a - The first vector.
      b - The second vector.
      c - The third vector.

    • setParticleMass

      public 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

    • setPointer

      public void setPointer(com.sun.jna.ptr.PointerByReference pointer)
      Set the pointer to the system.
      Parameters:
      pointer - The pointer to the system.

    • setVirtualSite

      public void setVirtualSite(int index, VirtualSite virtualSite)
      Set a particle to be a virtual site.
      Parameters:
      index - The index of the particle.
      virtualSite - The virtual site object.

    • usesPeriodicBoundaryConditions

      public boolean usesPeriodicBoundaryConditions()
      Check if the system uses periodic boundary conditions.
      Returns:
      True if the system uses periodic boundary conditions.