Merge pull request #2754 from peastman/benchmark

Updated benchmark script

Merge pull request #2754 from peastman/benchmark
Updated benchmark script
eec9cd69 · peastman · GitHub · 3fef456d · 6a82ea51 · eec9cd69
Unverified Commit eec9cd69 authored Jun 23, 2020 by peastman Committed by GitHub Jun 23, 2020
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examples/apoa1.pdb examples/apoa1.pdb +92385 -92575

examples/benchmark.py examples/benchmark.py +3 -2

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--- a/examples/apoa1.pdb
+++ b/examples/apoa1.pdb
--- a/examples/benchmark.py
+++ b/examples/benchmark.py
@@ -88,12 +88,13 @@ def runOneTest(testName, options):
            dt = 0.005*unit.picoseconds
            constraints = app.AllBonds
            hydrogenMass = 4*unit.amu
+            integ = mm.LangevinIntegrator(300*unit.kelvin, friction, dt)
        else:
-            dt = 0.002*unit.picoseconds
+            dt = 0.004*unit.picoseconds
            constraints = app.HBonds
            hydrogenMass = None
+            integ = mm.LangevinMiddleIntegrator(300*unit.kelvin, friction, dt)
        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))
    properties = {}
    initialSteps = 5