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OMMT absolute free energy of hydration: sol leg
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| from sys import stdout | |
| import sys, os | |
| from simtk import unit | |
| from simtk import openmm as omm | |
| import openmmtools as ommt | |
| import mdtraj | |
| #cache.global_context_cache.platform = openmm.Platform.getPlatformByName('CUDA') | |
| pdb = omm.app.PDBFile('lig.pdb') | |
| modeller = omm.app.Modeller(pdb.topology, pdb.positions) | |
| # add virtual sites | |
| forcefield = omm.app.ForceField('lig.xml', 'tip4pfb.xml') # tip3p tip4pew tip4pfb | |
| modeller.addExtraParticles(forcefield) | |
| modeller.addSolvent(forcefield, padding=1.6, model='tip4pew') | |
| system = forcefield.createSystem( | |
| modeller.topology, | |
| nonbondedMethod=omm.app.PME, | |
| nonbondedCutoff=1.2*unit.nanometer, | |
| constraints=omm.app.HBonds | |
| ) | |
| omm.app.PDBFile.writeFile(modeller.topology, modeller.positions, open("sol.pdb", "w")) | |
| # Define the region of the System to be alchemically modified | |
| mdtraj_top = mdtraj.Topology.from_openmm(modeller.topology) | |
| lig_atoms = mdtraj_top.select('resname LIG') | |
| print(f'Selected ligand: {lig_atoms}') | |
| # create the alchemical region | |
| factory = ommt.alchemy.AbsoluteAlchemicalFactory() | |
| alchemical_region = ommt.alchemy.AlchemicalRegion(alchemical_atoms=lig_atoms) | |
| print(f'Alchemical region: {alchemical_region}') | |
| alchemical_system = factory.create_alchemical_system(system, alchemical_region) | |
| alchemical_state = ommt.alchemy.AlchemicalState.from_system(alchemical_system) | |
| # define the lambdas and the protocol | |
| lambda_electrostatics = [1.00, 0.75, 0.50, 0.25] + [0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00] | |
| lambda_sterics = [1.00, 1.00, 1.00, 1.00, 1.00] + [0.95, 0.90, 0.8, 0.7, 0.6, 0.5, 0.4, 0.35, 0.3, 0.25, 0.2, 0.20, 0.1, 0.05, 0.00] | |
| protocol = {'lambda_electrostatics': lambda_electrostatics, | |
| 'lambda_sterics': lambda_sterics} | |
| # create the states for the replica exchange | |
| compound_states = ommt.states.create_thermodynamic_state_protocol( | |
| alchemical_system, | |
| protocol=protocol, | |
| composable_states=[alchemical_state], | |
| constants={'temperature': 298.0*unit.kelvin, 'pressure': 1.0*unit.atmosphere} | |
| ) | |
| # we define here 3k iterations for the entire RE sampler | |
| # use the default Langevin for every step (1 ps, 2fm step, 5.0/ps collision rate) | |
| simulation = ommt.multistate.ReplicaExchangeSampler(number_of_iterations=3000) | |
| reporter = ommt.multistate.MultiStateReporter('sol.nc', checkpoint_interval=1) | |
| # TODO add structure reporter | |
| simulation.create( | |
| thermodynamic_states=compound_states, | |
| sampler_states=ommt.states.SamplerState( | |
| modeller.positions, | |
| box_vectors=modeller.topology.getPeriodicBoxVectors()), | |
| storage=reporter | |
| ) | |
| simulation.run() | |
| print(simulation.iteration) | |
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