Reset step to 0 at beginning of each protocol
@@ -426,6 +426,7 @@ def run_nonequilibrium_switching(init_x, alchemical_integrator, nsteps, alchemic
alchemical_ctx.setPositions(init_x)
alchemical_ctx.setVelocitiesToTemperature(298 * unit.kelvin)
+ alchemical_integrator.setGlobalVariableByName("step", 0)
alchemical_integrator.step(nsteps)
return alchemical_integrator.getGlobalVariableByName("protocol_work")
