Simulation¶

The simulation finally connects a Topology with an EntityHandle. While applying minimization or md tasks, the current positions of the simulation object can be mapped back to the attached structure at any time.

class Simulation(entity, settings)¶

First constructor that takes an ost.mol.EntityHandle as an input and automatically constructs an internal Topology according to the provided settings. Be aware, that the entity will be altered depending on hydrogen/termini definitions in the Forcefield attached to the settings

Parameters:	entity (EntityHandle) – Entity from which a default Topology will be created according to the settings settings (Settings) – Controls the parametrization of the Simulation and the buildup of the internal Topology
Raises:	RuntimeError when construction of Topology fails

class Simulation(topology, entity, settings)

Second constructor that takes a Topology, a consistent ost.mol.EntityHandle and a Settings as input.

Parameters:	topology (Topology) – Topology to initialize the Simulation entity (EntityHandle) – Entity that is consistent with the provided topology settings (Settings) – Controls the parametrization of the Simulation
Raises:	RuntimeException when number of atoms in entity is not equal the number of particles in topology

Save(filename, settings)¶

Dumps current status of the simulation with its connected entity onto disk. All informations from the entity except plain chains, residues, atoms and bonds are lost.

Parameters:	filename (str) – Filename

Load(filename)¶

Loads a dumped simulation from disk. You have to make sure, that the provided settings are consistent with those from the saved simulation. Undefined behaviour must be expected otherwise.

Parameters:	filename (str) – Filename settings (Settings) – Settings to reparametrize loaded simulation

ApplyLBFGS([tolerance=1.0, max_iterations=1000])¶

Run minimization using the Limited-memory Broyden–Fletcher–Goldfarb–Shanno (L-BFGS) method.

Parameters:	tolerance (float) – Tolerance describing abort criteria of minimization. The tolerance is interpreted as the root mean square value of all force components. max_iterations (int) – Maximum number of minimization iterations

ApplySD([tolerance=100, max_iterations=1000])¶

Run minimization using the steepest descend method.

Parameters:	tolerance (float) – Tolerance describing abort criteria of minimization. The tolerance is interpreted as the norm of the maximum force acting onto the particles. max_iterations (int) – Maximum number of minimization iterations
Returns:	bool whether tolerance has been reached

Steps(steps)¶

Runs the simulation for steps number of steps.

Parameters:	steps (int) – Number of steps to perform

GetPositions([enforce_periodic_box = false, in_angstrom = true])¶

Parameters:	enforce_periodic_box (bool) – True if periodic box has to be enforced in_angstrom (bool) – True if positions should be in Angstrom, they’re in nm otherwise
Returns:	A ost.geom.Vec3List of all the positions of the atoms in the Entity.

SetPositions(positions[, in_angstrom = true])¶

Parameters:	positions (ost.geom.Vec3List) – Positions to be set in_angstrom (bool) – True if positions are in Angstrom, they’re expected to be in nm otherwise

UpdatePositions([enforce_periodic_box=false])¶

Sets the positions of the atoms in the EntityHandle to the current positions of the simulation.

Parameters:	enforce_periodic_box (bool) – True if periodic box should be enforced

GetVelocities()¶

Returns:	A Vec3List of all the velocities of the atoms in the Entity.

GetForces()¶

Returns:	A Vec3List of all the resulting forces for each atom in the Entity.

SetVelocities(velocities)¶

Parameters:	velocities (ost.geom.Vec3List) – Velocities to be set

GetEntity()¶

Returns:	EntityHandle attached to the simulation

GetEnergy()¶

Returns:	float Potential + Kinetic energy in kJ/mol of current simulation state

GetPotentialEnergy()¶

Returns:	float Potential energy in kJ/mol of current simulation state

GetKineticEnergy()¶

Returns:	float Kinetic energy in kJ/mol of current simulation state

GetTopology()¶

Returns:	Topology attached to the simulation

GetPeriodicBoxExtents()¶

Returns:	Vec3 Extents of the periodic box

SetPeriodicBoxExtents(vec)¶

Parameters:	vec (ost.geom.Vec3) – Periodic box extents in A

Register(observer)¶

Adds an observer to the simulation object. This can be used for example to write out the trajectory during the simulation.

Parameters:	observer (Observer) – Observer to be attached

AddPositionConstraint(index)¶

Fixes the position of the particle with index given in the argument.

Parameters:	index (int) – Particle to be fixed
Raises:	RuntimeError when index exceeds number of particles

AddPositionConstraints(indices)¶

Fixes the position of the atoms with the indices given in in the argument.

Parameters:	indices (list) – Particles to be fixed
Raises:	RuntimeError when an index in indices exceeds number of particles

ResetPositionConstraints()¶

Removes all position constraints.

ResetHarmonicBond(index, bond_length, force_constant)¶

Update of the harmonic bond parameters in the simulation and in the attached Topology

Parameters:	index (int) – Harmonic Bond to be reset bond_length (float) – New bond length in nm force_constant (float) – New force constant in kJ/mol/nm^2
Raises:	RuntimeError when index exceeds number of harmonic bonds

ResetHarmonicAngle()¶

Update of the harmonic angle parameters in the simulation and in the attached Topology

Parameters:	index (int) – Harmonic Angle to be reset angle (float) – New Angle in radians force_constant (float) – New force constant in kJ/mol/radian^2
Raises:	RuntimeError when index exceeds number of harmonic angles

ResetUreyBradleyAngle(index, angle, angle_force_constant, bond_length, bond_force_constant)¶

Update of the Urey-Bradley angle parameters in the simulation and in the attached Topology

Parameters:	index (int) – Urey-Bradley angle that has to be reset angle (float) – New angle in radians angle_force_constant (float) – New angle force constant kJ/mol/radian^2 bond_length (float) – New bond length in nm bond_force_constant (float) – New bond force constant in kJ/mol/nm^2
Raises:	RuntimeError when index exceeds number of urey-bradley angles

ResetPeriodicDihedral(index, multiplicity, phase, force_constant)¶

Update of the periodic dihedral parameters in the simulation and in the attached Topology

Parameters:	index (int) – Periodic dihedral to be reset multiplicity (int) – New Multiplicity phase (float) – New phase in radians force_constant (float) – New force constant in kJ/mol/radian^2
Raises:	RuntimeError when index exceeds number of periodic dihedrals

ResetPeriodicImproper(index, multiplicity, phase, force_constant)¶

Update of the periodic improper parameters in the simulation and in the attached Topology

Parameters:	index (int) – Periodic improper to be reset multiplicity (int) – New multiplicity phase (float) – New phase in radians force_constant (float) – New force constant kJ/mol/radian^2
Raises:	RuntimeError when index exceeds number of periodic impropers

ResetHarmonicImproper(index, phase, force_constant)¶

Update of the harmonic improper parameters in the simulation and in the attached Topology

Parameters:	index (int) – Harmonic improper to be reset phase (float) – New phase in radians force_constant (float) – New force constant kJ/mol/radian^2
Raises:	RuntimeError when index exceeds number of harmonic impropers

ResetLJPair(index, sigma, epsilon)¶

Update of the LJ pair parameters in the simulation and in the attached Topology

Parameters:	index (int) – LJ pair to be reset sigma (float) – New sigma in nm epsilon (float) – New epsilon in kJ/mol
Raises:	RuntimeError when index exceeds number of LJ pairs

ResetDistanceConstraint(index, constraint_length)¶

Update of the distance constraint parameters in the simulation and in the attached Topology

Parameters:	index (int) – Distance constraint to be reset constraint_length (float) – New constraint length in nm
Raises:	RuntimeError when index exceeds number of distance constraints

ResetHarmonicPositionRestraint(index, ref_position, force_constant, x_scale, y_scale, z_scale)¶

Update of the harmonic position restraint parameters in the simulation and in the attached Topology

Parameters:	index (int) – Harmonic position restraint to be reset ref_position (ost.geom.Vec3) – New reference position in nm force_constant (float) – New force constant in kJ/mol/nm^2 x_scale (float) – New x-scale y_scale (float) – New y-scale z_scale (float) – New z-scale
Raises:	RuntimeError when index exceeds number of harmonic position restraints

ResetHarmonicDistanceRestraint(index, length, force_constant)¶

Update of the harmonic distance restraint parameters in the simulation and in the attached Topology

Parameters:	index (int) – Harmonic distance restraint to be reset length (float) – New restraint length in nm force_constant (float) – New force constant kJ/mol/nm^2
Raises:	RuntimeError when index exceeds number of harmonic distance restraints

ResetLJ(index, sigma, epsilon)¶

Update of the lj parameters in the simulation and in the attached Topology

Parameters:	index (int) – LJ to be reset sigma (float) – New sigma in nm epsilon (float) – New epsilon in kJ/mol
Raises:	RuntimeError when index exceeds number of particles

ResetGBSA(index, radius, scaling)¶

Update of the GBSA parameters in the simulation and in the attached Topology

Parameters:	index (int) – : GB to be reset radius (float) – New radius in nm scaling (float) – New OBC scaling
Raises:	RuntimeError when index exceeds number of particles

ResetCharge(index, charge)¶

Update of the charge in the simulation and in the attached Topology

Parameters:	index (int) – Charge to be reset charge (float) – New Charge
Raises:	RuntimeError when index exceeds number of particles

ResetMass(index, mass)¶

Update of the mass in the simulation and in the attached Topology

Parameters:	index (int) – Mass to be reset mass (float) – New mass
Raises:	RuntimeError when index exceeds number of particles