Created simulateGromacs.py example

examples/simulateGromacs.py

+from simtk.openmm.app import *
+from simtk.openmm import *
+from simtk.unit import *
+from sys import stdout
+
+gro = GromacsGroFile('input.gro')
+top = GromacsTopFile('input.top', unitCellDimensions=gro.getUnitCellDimensions(), includeDir='/usr/local/gromacs/share/gromacs/top')
+system = top.createSystem(nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
+integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
+simulation = Simulation(top.topology, system, integrator)
+simulation.context.setPositions(gro.positions)
+simulation.minimizeEnergy()
+simulation.reporters.append(PDBReporter('output.pdb', 1000))
+simulation.reporters.append(StateDataReporter(stdout, 1000, step=True, potentialEnergy=True, temperature=True))
+simulation.step(10000)