min_crds[1] = min(min_crds[1], coord[1])
min_crds[2] = min(min_crds[2], coord[2])
max_crds[0] = max(max_crds[0], coord[0])
max_crds[1] = max(max_crds[1], coord[1])
max_crds[2] = max(max_crds[2], coord[2])
ala2_solv.box = [max_crds[0]-min_crds[0],
max_crds[1]-min_crds[1],
max_crds[2]-min_crds[2],
90.0, 90.0, 90.0]
# Create the OpenMM system
print('Creating OpenMM System')
system = ala2_solv.createSystem(params, nonbondedMethod=app.PME,
nonbondedCutoff=12.0*u.angstroms,
constraints=app.HBonds,
switchDistance=10.0*u.angstroms,
)
# Create the integrator to do Langevin dynamics
integrator = mm.LangevinIntegrator(
300*u.kelvin, # Temperature of heat bath
1.0/u.picoseconds, # Friction coefficient
2.0*u.femtoseconds, # Time step
)
# 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
min_crds[1] = min(min_crds[1], coord[1])
min_crds[2] = min(min_crds[2], coord[2])
max_crds[0] = max(max_crds[0], coord[0])
max_crds[1] = max(max_crds[1], coord[1])
max_crds[2] = max(max_crds[2], coord[2])
ala2_solv.setBox(max_crds[0]-min_crds[0],
max_crds[1]-min_crds[1],
max_crds[2]-min_crds[2],
)
# Create the OpenMM system
print('Creating OpenMM System')
system = ala2_solv.createSystem(params, nonbondedMethod=app.PME,
nonbondedCutoff=12.0*u.angstroms,
constraints=app.HBonds,
switchDistance=10.0*u.angstroms,
)
# Create the integrator to do Langevin dynamics
integrator = mm.LangevinIntegrator(
300*u.kelvin, # Temperature of heat bath
1.0/u.picoseconds, # Friction coefficient
2.0*u.femtoseconds, # Time step
)
# 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
params = CharmmParameterSet('toppar/par_all36_prot.prm')
ala5_gas = CharmmPsfFile('ala5_autopsf.psf')
ala5_crds = app.PDBFile('ala5_autopsf.pdb')
# NOTE NOTE
# The parameter set we used here is the CHARMM 36 force field, but this is
# strictly an example. It is important that you use the most accurate (typically
# most up-to-date) force fields for your own simulation. See the CHARMM
# parameter web page for updates:
# http://mackerell.umaryland.edu/CHARMM_ff_params.html
# END NOTE
# Create the OpenMM system
print('Creating OpenMM System')
system = ala5_gas.createSystem(params, nonbondedMethod=app.NoCutoff,
constraints=app.HBonds, implicitSolvent=app.HCT,
implicitSolventSaltConc=0.1*u.moles/u.liter,
)
# Create the integrator to do Langevin dynamics
integrator = mm.LangevinIntegrator(
300*u.kelvin, # Temperature of heat bath
1.0/u.picoseconds, # Friction coefficient
2.0*u.femtoseconds, # Time step
)
# 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
ala5_crds = app.PDBFile('ala5_autopsf.pdb')
# NOTE NOTE
# The parameter set we used here is the CHARMM 36 force field, but this is
# strictly an example. It is important that you use the most accurate (typically
# most up-to-date) force fields for your own simulation. See the CHARMM
# parameter web page for updates:
# http://mackerell.umaryland.edu/CHARMM_ff_params.html
# END NOTE
# Create the OpenMM system
print('Creating OpenMM System')
system = ala5_gas.createSystem(
params,
nonbondedMethod=app.NoCutoff,
constraints=app.HBonds,
implicitSolvent=app.HCT,
implicitSolventSaltConc=0.1 * u.moles / u.liter,
)
# Create the integrator to do Langevin dynamics
integrator = mm.LangevinIntegrator(
300 * u.kelvin, # Temperature of heat bath
1.0 / u.picoseconds, # Friction coefficient
2.0 * u.femtoseconds, # Time step
)
# 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
