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Commit 6a82ea51 authored by Peter Eastman's avatar Peter Eastman
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Updated benchmark script

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examples/apoa1.pdb
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examples/benchmark.py
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...@@ -88,12 +88,13 @@ def runOneTest(testName, options): ...@@ -88,12 +88,13 @@ def runOneTest(testName, options):
dt = 0.005*unit.picoseconds dt = 0.005*unit.picoseconds
constraints = app.AllBonds constraints = app.AllBonds
hydrogenMass = 4*unit.amu hydrogenMass = 4*unit.amu
integ = mm.LangevinIntegrator(300*unit.kelvin, friction, dt)
else: else:
dt = 0.002*unit.picoseconds dt = 0.004*unit.picoseconds
constraints = app.HBonds constraints = app.HBonds
hydrogenMass = None hydrogenMass = None
integ = mm.LangevinMiddleIntegrator(300*unit.kelvin, friction, dt)
system = ff.createSystem(pdb.topology, nonbondedMethod=method, nonbondedCutoff=cutoff, constraints=constraints, hydrogenMass=hydrogenMass) system = ff.createSystem(pdb.topology, nonbondedMethod=method, nonbondedCutoff=cutoff, constraints=constraints, hydrogenMass=hydrogenMass)
integ = mm.LangevinIntegrator(300*unit.kelvin, friction, dt)
print('Step Size: %g fs' % dt.value_in_unit(unit.femtoseconds)) print('Step Size: %g fs' % dt.value_in_unit(unit.femtoseconds))
properties = {} properties = {}
initialSteps = 5 initialSteps = 5
......
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