def load_alanine(constrained=True):
"""Load AlanineDipeptide vacuum, optionally with hydrogen bonds constrained"""
if constrained: constraints = app.HBonds
else: constraints = None
testsystem = AlanineDipeptideVacuum(constraints=constraints)
topology, system, positions = testsystem.topology, testsystem.system, testsystem.positions
keep_only_some_forces(system)
return topology, system, positions
def load_t4_implicit(constrained=True):
if constrained:
constraints = app.HBonds
else:
constraints = None
testsystem = LysozymeImplicit(constraints=constraints,
implicitSolvent=app.OBC2)
topology, system, positions = testsystem.topology, testsystem.system, testsystem.positions
keep_only_some_forces(system, extra_forces_to_keep=["GBSAOBCForce"])
return topology, system, positions
def load_src_explicit(constrained=True):
if constrained:
constraints = app.HBonds
rigid_water = True
else:
constraints = None
rigid_water = False
testsystem = SrcExplicit(constraints=constraints, rigid_water=rigid_water)
topology, system, positions = testsystem.topology, testsystem.system, testsystem.positions
keep_only_some_forces(system)
add_barostat(system)
return topology, system, positions
def load_dhfr_reaction_field(constrained=True):
"""DHFR in explicit solvent, but using reaction field instead of PME for nonbonded"""
if constrained:
constraints = app.HBonds
rigid_water = True
else:
constraints = None
rigid_water = False
testsystem = DHFRExplicit(nonbondedCutoff=15 * unit.angstrom,
nonbondedMethod=app.CutoffPeriodic,
constraints=constraints,
rigid_water=rigid_water)
topology, system, positions = testsystem.topology, testsystem.system, testsystem.positions
keep_only_some_forces(system)
system = replace_reaction_field(system, shifted=True)
add_barostat(system)
return topology, system, positions