meld.system.openmm_runner.transform

Transformers are objects that take an openmm system as created by loading an amber topology and modify it in various ways. Example transformations include: - Adding extra forces for restraints - Modifying an existing force, like REST2 - Replacing an existing force, like softcore interactions

One thing transformers should not do is add particles to the system. Instead, particles can be added using Patcher objects.

The transformers are chained together, so that at the end, all necessary modifications have been made and the system can be simulated with OpenMM. To add a new transformer, you must first create a new transformer class that implements the transformer protocol given in TransformerBase. Next, you must add this class to the list in OpenMMRunner._setup_transformers.

Classes

TransformerBase(options, …)

Base class to document how transformers work.

class meld.system.openmm_runner.transform.TransformerBase(options, always_active_restraints, selectively_active_restraints)[source]

Base class to document how transformers work.

The transformation process proceeds in several stages. - The transformer is initialized with the run options and lists of restraints. The transformer must store any relevant information, as these parameters will not be given again. The __init__ method must also delete any restraints that are handled by this transformer from always_active_restraints and selectively_active_restraints. - Next, add_interactions is called. This provides an opportunity for the transformer to add new forces, or to modify or replace existing forces. - Next finalize is called. All changes to particles and forces are completed before this call, which can be useful when we have to, e.g. store parameters. - Finally, update is called every stage. This provides an opportunity to update parameters like force constants depending on alpha or on the time step.

The number of particles cannot be changed by a transformer, instead additional particles should be added using a patcher.

Parameters
  • options (meld.system.RunOptions) – the options for the runner

  • always_active_restraints (list of restraints) – these restraints are always active

  • selectively_active_collections (list of SelectivelyActiveCollection) – these restraints are selected by the MELD algorithm

add_interactions(system, topology)[source]

Add new interactions to the system.

This may involve: - Adding new forces, e.g. for restraints - Replacing an existing force with another, e.g. softcore

interactions

This method must return the modified system. If the transformer does not add interactions, it may simply return the passed values.

Parameters
  • system (simtk.openmm.System) – OpenMM system object to be modified

  • topology (simtk.openmm.Topology) – OpenMM topology object to be modified and/or used for indexing

finalize(system, topology)[source]

Finalize the transformer.

This method is guaranteed to be called after all forces are added to the system and provides an opportunity to do bookkeeping.

This method should not add any new forces.

Parameters
  • system (simtk.openmm.System) – OpenMM system object to be modified

  • topology (simtk.openmm.Topology) – OpenMM topology object to be modified and/or used for indexing

update(simulation, alpha, timestep)[source]

Update the system according to alpha and timestep.

This method is called at the beginning of every stage. It should update forces and parameters as necessary.

Parameters
  • simulation (simtk.openmm.app.simulation) – OpenMM simulation object to be modified

  • alpha (float) – Current value of alpha, ranges from 0 to 1

  • stage (int) – Current stage of the simulation, starting from 0