from paprika.amber import Simulation import logging logging.basicConfig( filename='tscc.log', 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
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
datefmt="%Y-%m-%d %I:%M:%S %p", level=logging.DEBUG, ) 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")) with open("n_atoms.dat", "r") as f: ntwprt = int(f.read()) 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