def load_waterbox(constrained=True):
"""Load WaterBox test system"""
testsystem = WaterBox(constrained=constrained)
(topology, system,
positions) = testsystem.topology, testsystem.system, testsystem.positions
add_barostat(system)
return topology, system, positions
def load_solvated_alanine(constrained=True):
"""Load AlanineDipeptide in explicit solvent,
optionally with rigid water + hydrogen bonds constrained."""
if constrained:
testsystem = AlanineDipeptideExplicit(constraints=app.HBonds, rigid_water=True)
else:
testsystem = AlanineDipeptideExplicit(constraints=None, rigid_water=False)
topology, system, positions = testsystem.topology, testsystem.system, testsystem.positions
add_barostat(system)
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
topology=top,
system=sys,
positions=pos,
temperature=temperature,
timestep=0.5 * unit.femtosecond,
burn_in_length=200000,
n_samples=1000,
thinning_interval=20000,
name="flexible_waterbox")
# add a smaller waterbox, for the purposes of comparison of the inefficient nested estimator
# against the efficient near-equilibrium estimator
small_box_edge = 15 * unit.angstrom
testsystem = WaterBox(
box_edge=small_box_edge,
cutoff=small_box_edge / 2.5, # box_edge must be > (2 * cutoff)
)
(top, sys, pos) = testsystem.topology, testsystem.system, testsystem.positions
add_barostat(sys)
tiny_waterbox = EquilibriumSimulator(platform=configure_platform("CUDA"),
topology=top,
system=sys,
positions=pos,
temperature=temperature,
timestep=1.0 * unit.femtosecond,
burn_in_length=100000,
n_samples=1000,
thinning_interval=10000,
name="tiny_waterbox_constrained")