# import OpenSMOG from OpenSMOG import SBM #Choose some basic runtime settings. We will call our system 2ci2 SMOGrun = SBM(name='3p63', time_step=0.002, collision_rate=1.0, r_cutoff=0.65, temperature=0.5) #Select a platform and GPU IDs (if needed) #We will use opencl. If you want to perform CPU-only calculations, set platform to 'CPU'. SMOGrun.setup_openmm(platform='opencl',GPUindex='default') #Decide where to save your data (here, output_2ci2) SMOGrun.saveFolder('output_3p63') #You may optionally set some input file names to variables SMOG_grofile = '3p63.OpenSMOG.AA+novelLigand.gro' SMOG_topfile = '3p63.OpenSMOG.AA+novelLigand.top' SMOG_xmlfile = '3p63.OpenSMOG.AA+novelLigand.xml' #Load your force field data SMOGrun.loadSystem(Grofile=SMOG_grofile, Topfile=SMOG_topfile, Xmlfile=SMOG_xmlfile) #Create the context, and prepare the simulation to run SMOGrun.createSimulation() #Perform L-BFGS energy minimization SMOGrun.minimize(tolerance=1) #Decide how frequently to save data SMOGrun.createReporters(trajectory=True, energies=True, energy_components=True, interval=10**3) #Launch the simulation SMOGrun.run(nsteps=10**6, report=True, interval=10**3) #Note: One can also run for clock time, rather than number of timesteps. For example, to run for 10 hours, you could use: SMOGrun.runForClockTime(time=10)