StateDataReporter('relax-hydrogens.log',
1000,
step=True,
temperature=True,
potentialEnergy=True,
totalEnergy=True,
speed=True))
minimize.step(min_steps)
print("Done 100000 steps of minimization.")
print("Potential energy after minimization:")
#print(minimize.context.getState(getEnergy=True).getPotentialEnergy())
positions = minimize.context.getState(getPositions=True).getPositions()
print("Done updating positions.")
#velocities = minimize.context.getState(getVelocities=True).getVelocities()
#print("Done updating velocities.")
minimize.saveCheckpoint('state.chk')
print("Done saving checkpoints.")
# update the current context with changes in system
# minimize.context.reinitialize(preserveState=True)
# output the minimized protein as a shortcut
PDBFile.writeFile(molecule.topology,
positions,
open(f'{pdbid}_chain{chain}_minimized.pdb', 'w'),
keepIds=True)
print("Done outputing minimized pdb.")
# clean the context
del minimize.context
# directly load the minimized protein
pdb = PDBFile(f'{pdbid}_chain{chain}_minimized.pdb')
molecule = Modeller(pdb.topology, pdb.positions)
# load force field
print("Done setting tolerance.")
simulation.minimizeEnergy(tolerance=tolerance, maxIterations=1000)
print("Done setting energy minimization.")
simulation.reporters.append(
StateDataReporter('relax-hydrogens.log',
1000,
step=True,
temperature=True,
potentialEnergy=True,
totalEnergy=True,
speed=True))
simulation.step(10000)
print("Done 10000 steps of simulation.")
positions = simulation.context.getState(getPositions=True).getPositions()
print("Done updating positions.")
simulation.saveCheckpoint('state.chk')
print("Done saving checkpoints.")
# update the current context with changes in system
simulation.context.reinitialize()
# Set up the context for mtd simulation
# at this step the CV and the system are separately passed to Metadynamics
meta = mtd.Metadynamics(system, [bv],
310.15 * unit.kelvin,
6.0,
1.2 * unit.kilojoules_per_mole,
500,
saveFrequency=500,
biasDir='./biases')
integrator = mm.LangevinIntegrator(310.15 * unit.kelvin, 1.0 / unit.picosecond,
0.002 * unit.picoseconds)
