def test_amber_minimization(clean_files):
simulation = Simulation()
simulation.path = os.path.join("tmp")
shutil.copy(os.path.join(os.path.dirname(__file__), "../data/k-cl/k-cl.prmtop"), "tmp")
shutil.copy(os.path.join(os.path.dirname(__file__), "../data/k-cl/k-cl.rst7"), "tmp")
simulation.executable = "sander"
simulation.restraint_file = None
simulation.prefix = "minimize"
simulation.topology = "k-cl.prmtop"
simulation.inpcrd = "k-cl.rst7"
simulation.config_gb_min()
# Turn off GB for now.
simulation.cntrl["igb"] = 0
simulation.cntrl["ntb"] = 0
simulation.run()
mdout = parse_mdout(os.path.join("tmp", "minimize.out"))
assert pytest.approx(mdout["Bond"][-1]) == 0
assert pytest.approx(mdout["Angle"][-1]) == 0
assert pytest.approx(mdout["Dihedral"][-1]) == 0
assert pytest.approx(mdout["V14"][-1]) == 0
assert pytest.approx(mdout["E14"][-1]) == 0
assert pytest.approx(mdout["VDW"][0], 0.1) == 6.5734
assert pytest.approx(mdout["Ele"][0], 0.1) == -211.7616
format='%(asctime)s %(message)s',
datefmt='%Y-%m-%d %I:%M:%S %p',
level=logging.DEBUG)
logging.info('Started logging...')
logging.info(paprika.__version__)
ntwprt = 206
nstlim = 500000
sim = Simulation()
# Minimization
sim.executable = 'pmemd.cuda'
sim.topology = 'solvate.prmtop'
sim.prefix = 'minimize'
sim.inpcrd = 'solvate.rst7'
sim.path = './'
sim.ref = 'solvate.rst7'
sim.config_pbc_min()
sim.cntrl['maxcyc'] = 500
sim.cntrl['ncyc'] = 400
sim.cntrl['ntr'] = 1
sim.cntrl['restraint_wt'] = 50.0
sim.cntrl['restraintmask'] = "'@DUM'"
sim.cntrl['cut'] = 9.0
sim.restraint_file = 'disang.rest'
sim.run(fail_ok=False)
# Equilibration
sim.config_pbc_md()
sim.executable = 'pmemd.cuda'
ntwprt = 204
nstlim = 500000
sim = Simulation()
# Production
for iteration in range(0, 20):
sim.executable = 'pmemd.cuda'
sim.path = './'
sim.topology = 'solvate.prmtop'
sim.restraint_file = 'disang.rest'
sim.config_pbc_md()
sim.prefix = 'prod.{:03d}'.format(iteration)
if iteration == 0:
sim.inpcrd = 'equil.rst7'
else:
sim.inpcrd = 'prod.{:03d}.rst7'.format(iteration - 1)
sim.ref = 'solvate.rst7'
sim.cntrl['ntx'] = 5
sim.cntrl['irest'] = 1
sim.cntrl['nstlim'] = nstlim
sim.cntrl['ntwr'] = nstlim
sim.cntrl['ntwx'] = 250
sim.cntrl['ntwprt'] = ntwprt
sim.cntrl['ntxo'] = 2
sim.restraint_file = 'disang.rest'
sim.run(fail_ok=False)
logging.info("Started logging...")
logging.info(paprika.__version__)
hostname = sp.check_output(["hostname"])
nvidia_smi = sp.check_output(["nvidia-smi"])
logging.info(hostname.decode("utf-8"))
logging.info(nvidia_smi.decode("utf-8"))
nstlim = 500000
sim = Simulation()
# Minimization
sim.executable = "pmemd.cuda"
sim.topology = "smirnoff.prmtop"
sim.prefix = "minimize"
sim.inpcrd = "smirnoff.inpcrd"
sim.path = "./"
sim.ref = "smirnoff.inpcrd"
sim.config_pbc_min()
sim.cntrl["maxcyc"] = 500
sim.cntrl["ncyc"] = 400
sim.cntrl["ntr"] = 1
sim.cntrl["restraint_wt"] = 50.0
sim.cntrl["restraintmask"] = "'@Pb'"
sim.cntrl["cut"] = 9.0
sim.restraint_file = "disang.rest"
sim.run(fail_ok=False)
# Equilibration
sim.config_pbc_md()
sim.executable = "pmemd.cuda"
def test_amber_single_window_gbmin(clean_files):
# Distance restraint
restraint = restraints.DAT_restraint()
restraint.continuous_apr = True
restraint.amber_index = True
restraint.topology = os.path.join(
os.path.dirname(__file__), "../data/k-cl/k-cl.pdb"
)
restraint.mask1 = ":K+"
restraint.mask2 = ":Cl-"
restraint.attach["target"] = 4.5
restraint.attach["fraction_list"] = [0.00, 0.04, 0.181, 0.496, 1.000]
restraint.attach["fc_final"] = 5.0
restraint.pull["fc"] = restraint.attach["fc_final"]
restraint.pull["target_initial"] = restraint.attach["target"]
restraint.pull["target_final"] = 18.5
restraint.pull["num_windows"] = 5
restraint.initialize()
windows_directory = os.path.join("tmp", "k-cl", "windows")
window_list = create_window_list([restraint])
for window in window_list:
os.makedirs(os.path.join(windows_directory, window))
with open(
os.path.join(windows_directory, window, "restraints.in"), "a"
) as file:
string = amber.amber_restraint_line(restraint, window)
file.write(string)
for window in window_list:
if window[0] == "a":
structure = pmd.load_file(
os.path.join(os.path.dirname(__file__), "../data/k-cl/k-cl-sol.prmtop"),
os.path.join(os.path.dirname(__file__), "../data/k-cl/k-cl-sol.rst7"),
structure=True,
)
for atom in structure.atoms:
if atom.name == "Cl-":
atom.xz = 2.65
structure.save(
os.path.join(windows_directory, window, "k-cl.prmtop"), overwrite=True
)
structure.save(
os.path.join(windows_directory, window, "k-cl.rst7"), overwrite=True
)
structure.save(
os.path.join(windows_directory, window, "k-cl.pdb"), overwrite=True
)
elif window[0] == "p":
structure = pmd.load_file(
os.path.join(os.path.dirname(__file__), "../data/k-cl/k-cl-sol.prmtop"),
os.path.join(os.path.dirname(__file__), "../data/k-cl/k-cl-sol.rst7"),
structure=True,
)
target_difference = (
restraint.phase["pull"]["targets"][int(window[1:])]
- restraint.phase["pull"]["targets"][0]
)
for atom in structure.atoms:
if atom.name == "Cl-":
atom.xz += target_difference
structure.save(
os.path.join(windows_directory, window, "k-cl.prmtop"), overwrite=True
)
structure.save(
os.path.join(windows_directory, window, "k-cl.rst7"), overwrite=True
)
structure.save(
os.path.join(windows_directory, window, "k-cl.pdb"), overwrite=True
)
gbsim = Simulation()
gbsim.path = os.path.join("tmp", "k-cl", "windows", "a003")
gbsim.executable = "sander"
gbsim.topology = "k-cl.prmtop"
gbsim.prefix = "minimize"
gbsim.inpcrd = "k-cl.rst7"
gbsim.config_gb_min()
gbsim.cntrl["maxcyc"] = 1
gbsim.cntrl["ncyc"] = 1
gbsim.run()
gbsim.config_gb_md()
gbsim.prefix = "md"
gbsim.inpcrd = "minimize.rst7"
gbsim.cntrl["nstlim"] = 1
gbsim.cntrl["ntwe"] = 1
gbsim.cntrl["ntpr"] = 1
gbsim.cntrl["ig"] = 777
gbsim.run()
mden = parse_mden(os.path.join("tmp", "k-cl", "windows", "a003", "md.mden"))
assert pytest.approx(mden["Bond"][0]) == 0
assert pytest.approx(mden["Angle"][0]) == 0
assert pytest.approx(mden["Dihedral"][0]) == 0
assert pytest.approx(mden["V14"][0]) == 0
assert pytest.approx(mden["E14"][0]) == 0
assert pytest.approx(mden["VDW"][0], 0.1) == 25956.13225
assert pytest.approx(mden["Ele"][0], 0.1) == -18828.99631
assert pytest.approx(mden["Total"][0], 0.1) == 7127.13594