Remove test that was no longer being run
@@ -686,40 +686,6 @@ def run_alchemical_langevin_integrator(nsteps=0, splitting="O { V R H R V } O"):
if nsigma > NSIGMA_MAX:
raise Exception("The free energy difference for the nonequilibrium switching for splitting '%s' and %d steps is not zero within statistical error." % (splitting, nsteps))
-def run_nonequilibrium_switching(init_x, alchemical_integrator, nsteps, alchemical_ctx, temperature=298 * unit.kelvin):
- """Perform a nonequilibrium switching protocol
-
- Parameters
- ----------
- init_x : simtk.openmm.Quantity of size [natoms,3] with units compatible with angstroms
- Initial positions
- alchemical_integrator : AlchemicalNonequilibriumLangevinIntegrator
- Integrator to use for switching
- alchemical_ctx : simtk.openmm.Context
- Context to use for alchemical switching.
- temperature : simtk.unit.Quantity, optional, default=298*kelvin
- Temperature to initialize simulation with
-
- Returns
- -------
- protocol_work : float
- Work performed by protocol
- """
- # Get number of NCMC steps
- nsteps = alchemical_integrator.getGlobalVariableByName("nsteps")
- # Set positions and velocities
- alchemical_ctx.setPositions(init_x)
- alchemical_ctx.setVelocitiesToTemperature(temperature)
- # Reset the integrator
- alchemical_integrator.reset_integrator()
- if (nsteps == 0):
- # We still need to take one step if nsteps == 0
- alchemical_integrator.step(1)
- else:
- alchemical_integrator.step(nsteps)
- # Get the protocol work in dimensionless units (kT)
- return alchemical_integrator.getGlobalVariableByName("protocol_work") # in kT
-
def test_alchemical_langevin_integrator():
for splitting in ["O { V R H R V } O", "O V R H R V O", "H R V O V R H"]:
for nsteps in [0, 1, 10]:
