Created simulateGromacs.py example

5e6d705e · Peter Eastman · e4b38cce · 5e6d705e · 5e6d705e · 5e6d705e
Commit 5e6d705e authored Apr 17, 2013 by Peter Eastman
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examples/input.gro examples/input.gro +8870 -0

examples/input.top examples/input.top +5553 -0

examples/simulateGromacs.py examples/simulateGromacs.py +15 -0

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--- a/examples/input.gro
+++ b/examples/input.gro
--- a/examples/input.top
+++ b/examples/input.top
--- a/examples/simulateGromacs.py
+++ b/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)