This package contains factories for creating alchemically-modified versions of OpenMM systems.
The easiest way to install is through the conda package manager through the omnia binstar repository:
conda install -c omnia alchemyCreate alchemical intermediates for p-xylene binding to T4 lysozyme L99A in implicit solvent.
# Create a reference system for T4 lysozyme L99A
from openmmtools import testsystems
complex = testsystems.LysozymeImplicit()
[reference_system, positions] = [complex.system, complex.positions]
receptor_atoms = range(0,2603) # T4 lysozyme L99A
ligand_atoms = range(2603,2621) # p-xylene
# Create a factory to produce alchemical intermediates.
factory = AbsoluteAlchemicalFactory(reference_system, ligand_atoms=ligand_atoms)
# Get the default protocol for 'denihilating' in complex in implicit solvent.
protocol = factory.defaultComplexProtocolImplicit()
# Create the perturbed systems using this protocol.
systems = factory.createPerturbedSystems(protocol)Alchemical softcore parameters are now exposed as context parameters, and can be tweaked on the fly. The default selection of softcore c was also changed.
This release allows specified bonds, angles, and torsions to be alchemically softened. 1.1.1 was a critical bugfix release.
This release breaks out alchemy.py from the yank project