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