meld.runner.transform.rest2.REST2Transformer

class meld.runner.transform.rest2.REST2Transformer(param_manager, mapper, density_manager, builder_info, options, always_active_restraints, selectively_active_restraints)[source]

Bases: TransformerBase

An implementation of REST2

We use the updated version of Replica Exchange with Solute Scaling.

Warning

Currently, the REST2 implmentation in MELD has a limitation that any CMAP / AMAP potentials are not scaled.

References

L. Wang, R.A. Friesner, B.J. Berne, Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering.

__init__(param_manager, mapper, density_manager, builder_info, options, always_active_restraints, selectively_active_restraints)[source]

Initialize a Transformer

Parameters

  • param_manager (ParameterManager) – parameter manager to handle sampling of paramters

  • builder_info (dict) – information from the system builder / patcher

  • options (RunOptions) – the options for the runner

  • always_active_restraints (List[Restraint]) – these restraints are always active

  • selectively_active_collections – these restraints are selected by the MELD algorithm

Methods

__init__(param_manager, mapper, ...)

Initialize a Transformer

add_interactions(state, system, topology)

Add new interactions to the system.

finalize(state, system, topology)

Finalize the transformer.

update(state, simulation, alpha, timestep)

Update the system according to alpha and timestep.

Attributes

scaler

ramp

nb_force

dihedral_force

protein_nonbonded_params

protein_exception_params

protein_dihedrals

finalize(state, 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

  • state (IState) – the state of the system

  • system (System) – OpenMM system object to be modified

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

Return type

None

update(state, 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

  • state (IState) – the state of the system

  • simulation (Simulation) – OpenMM simulation object to be modified

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

  • stage – current stage of the simulation, starting from 0

Return type

None