Minor patch

bin/openmm-runner.py

@@ -10,21 +10,27 @@
 modeller = Modeller(pdb.topology, pdb.positions)
 modeller.deleteWater()
 residues=modeller.addHydrogens(forcefield)
-modeller.addSolvent(forcefield, numAdded=sys.argv[4])
+solvmol=int(sys.argv[4])
+modeller.addSolvent(forcefield, numAdded=solvmol)
 system = forcefield.createSystem(modeller.topology, nonbondedMethod=PME, nonbondedCutoff=1.0*nanometer, constraints=HBonds)
-integrator = LangevinMiddleIntegrator(sys.argv[2]*kelvin, 1/picosecond, 0.004*picoseconds)
+temp=int(sys.argv[2])
+integrator = LangevinMiddleIntegrator(temp*kelvin, 1/picosecond, 0.004*picoseconds)
 simulation = Simulation(modeller.topology, system, integrator)
 simulation.context.setPositions(modeller.positions)
 print("Minimizing energy")
 simulation.minimizeEnergy()
 print("Running NVT")
-simulation.reporters.append(PDBReporter(sys.argv[8], sys.argv[7]))
-simulation.reporters.append(StateDataReporter(stdout, sys.argv[7], step=True,
+reprate=int(sys.argv[7])
+simulation.reporters.append(PDBReporter(sys.argv[8], reprate))
+simulation.reporters.append(StateDataReporter(stdout, reprate, step=True,
         potentialEnergy=True, temperature=True, volume=True))
-simulation.reporters.append(StateDataReporter(sys.argv[9], sys.argv[7], step=True,
+simulation.reporters.append(StateDataReporter(sys.argv[9], reprate, step=True,
         potentialEnergy=True, temperature=True, volume=True))
-simulation.step(sys.argv[5])
-system.addForce(MonteCarloBarostat(sys.argv[3]*bar, sys.argv[2]*kelvin))
+nvtsteps=int(sys.argv[5])
+pres=sys.argv[3]
+simulation.step(nvtsteps)
+system.addForce(MonteCarloBarostat(pres*bar, temp*kelvin))
 simulation.context.reinitialize(preserveState=True)
 print("Running NPT")
-simulation.step(sys.argv[6])
+nptsteps=int(sys.argv[6])
+simulation.step(nptsteps)

bin/plot.py

@@ -8,7 +8,8 @@
 potential_energy = data[:,1]
 temperature = data[:,2]
 volume = data[:,3]
-clipped_step = (data[:,0] > sys.argv[2])
+skipsteps = int(sys.argv[2])
+clipped_step = (data[:,0] > skipsteps)
 clipped_data = data[clipped_step]
 
 clipped_pe = np.array(clipped_data[0:,1])