)
# Define the platform to use; CUDA, OpenCL, CPU, or Reference. Or do not specify
# the platform to use the default (fastest) platform
platform = mm.Platform.getPlatformByName('CUDA')
prop = dict(CudaPrecision='mixed') # Use mixed single/double precision
# Create the Simulation object
sim = app.Simulation(ala5_gas.topology, system, integrator, platform, prop)
# Set the particle positions
sim.context.setPositions(ala5_gas.positions)
# Minimize the energy
print('Minimizing energy')
sim.minimizeEnergy(maxIterations=500)
# Set up the reporters to report energies and coordinates every 100 steps
sim.reporters.append(
AmberStateDataReporter(sys.stdout, 100, step=True, potentialEnergy=True,
kineticEnergy=True, temperature=True)
)
sim.reporters.append(
NetCDFReporter('ala5_gb.nc', 100, atom=ala5_gas.ptr('natom'),
uses_pbc=False, crds=True)
)
# Run dynamics
print('Running dynamics')
sim.step(10000)
# Define the platform to use; CUDA, OpenCL, CPU, or Reference. Or do not specify
# the platform to use the default (fastest) platform
platform = mm.Platform.getPlatformByName('CUDA')
prop = dict(CudaPrecision='mixed') # Use mixed single/double precision
# Create the Simulation object
sim = app.Simulation(ala2_solv.topology, system, integrator, platform, prop)
# Set the particle positions
sim.context.setPositions(ala2_solv.positions)
# Minimize the energy
print('Minimizing energy')
sim.minimizeEnergy(maxIterations=500)
# Set up the reporters to report energies and coordinates every 100 steps
sim.reporters.append(
AmberStateDataReporter(sys.stdout, 100, step=True, potentialEnergy=True,
kineticEnergy=True, temperature=True,
volume=True, density=True)
)
sim.reporters.append(
NetCDFReporter('ala2_solv.nc', 100, atom=ala2_solv.ptr('natom'),
uses_pbc=True, crds=True)
)
# Run dynamics
print('Running dynamics')
sim.step(10000)
