Non-specified kinetic energy variable in addGHMCStep
In https://github.com/choderalab/perses/blob/master/perses/annihilation/ncmc_switching.py#L911-L922 there are two kinetic energy variables, "kinetic" and "ke". However ke is never actually added to the set of global variables so it causes the NCMCGHMCAlchemicalIntegrator to behave improperly.
diff --git a/perses/annihilation/ncmc_switching.py b/perses/annihilation/ncmc_switching.py
index baadec37..4b6c0da7 100644
--- a/perses/annihilation/ncmc_switching.py
+++ b/perses/annihilation/ncmc_switching.py
@@ -918,7 +918,7 @@ class NCMCAlchemicalIntegrator(openmm.CustomIntegrator):
         self.addConstrainPositions()
         self.addComputePerDof("v", "v + 0.5*dt*f/m + (x-x1)/dt")
         self.addConstrainVelocities()
-        self.addComputeSum("ke", "0.5*m*v*v")
+        self.addComputeSum("kinetic", "0.5*m*v*v")
         self.addComputeGlobal("Enew", "kinetic + energy")
         # Compute acceptance probability
         self.addComputeGlobal("accept", "step(exp(-(Enew-Eold)/kT) - uniform)")
['perses/annihilation/ncmc_switching.py']