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
# 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' sim.topology = 'solvate.prmtop' sim.path = './' sim.restraint_file = 'disang.rest' sim.cntrl['nstlim'] = nstlim sim.cntrl['ntwx'] = 250 sim.cntrl['ntwprt'] = ntwprt sim.cntrl['ntwr'] = 250 sim.cntrl['cut'] = 9.0
# 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" sim.topology = "smirnoff.prmtop" sim.path = "./" sim.restraint_file = "disang.rest" sim.cntrl["nstlim"] = nstlim sim.cntrl["ntwx"] = 250 sim.cntrl["ntwr"] = 250 sim.cntrl["cut"] = 9.0 iteration = 0