def test_tip3p_with_dispersion():
logger.info("Creating TIP3P explicit system with dispersion correction...")
system_container = testsystems.WaterBox(dispersion_correction=True)
(reference_system, positions) = system_container.system, system_container.positions
natoms = reference_system.getNumParticles()
ligand_atoms = range(0,3) # alanine residue
receptor_atoms = range(3,natoms) # one water
alchemical_factory_check(reference_system, positions, receptor_atoms, ligand_atoms)
logger.info("")
def notest_tip3p_pme(): # DISABLED because PME support is not working
logger.info(
"====================================================================")
logger.info("Creating TIP3P explicit system using PME...")
system_container = testsystems.WaterBox(dispersion_correction=False,
nonbondedMethod=app.PME)
(reference_system,
positions) = system_container.system, system_container.positions
natoms = reference_system.getNumParticles()
ligand_atoms = range(0, 3) # alanine residue
receptor_atoms = range(3, natoms) # one water
alchemical_factory_check(reference_system, positions, receptor_atoms,
ligand_atoms)
logger.info(
"====================================================================")
logger.info("")
def test_tip3p_reaction_field():
logger.info(
"====================================================================")
logger.info("Creating TIP3P explicit system using reaction field...")
system_container = testsystems.WaterBox(dispersion_correction=False,
switch=True,
nonbondedMethod=app.CutoffPeriodic)
(reference_system,
positions) = system_container.system, system_container.positions
natoms = reference_system.getNumParticles()
ligand_atoms = range(0, 3) # alanine residue
receptor_atoms = range(3, natoms) # one water
alchemical_factory_check(reference_system, positions, receptor_atoms,
ligand_atoms)
logger.info(
"====================================================================")
logger.info("")