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'
sim.topology = 'solvate.prmtop'
sim.path = './'
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"
sim.topology = "smirnoff.prmtop"
sim.path = "./"