Updated benchmark script

6a82ea51 · Peter Eastman · 3fef456d · 6a82ea51 · 6a82ea51
Commit 6a82ea51 authored Jun 22, 2020 by Peter Eastman
Show whitespace changes
Inline Side-by-side

Showing with 92388 additions and 92577 deletions

examples/apoa1.pdb examples/apoa1.pdb +92385 -92575

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

No files found.
--- 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