[BUG] Matching energies to reference after dynamics about dmff HOT 2 CLOSED

import sys
import time
import jax
import jax.numpy as jnp
import numpy as np
import openmm.app as app
import openmm.unit as unit
import openmm as mm
from dmff import Hamiltonian, NeighborListFreud

from jax.config import config
config.update("jax_enable_x64", True)

prmtop = app.AmberPrmtopFile("RAMP1_gas.prmtop")
inpcrd = app.AmberInpcrdFile("RAMP1_gas.inpcrd")
ff = Hamiltonian("amber14/protein.ff14SB.xml", "amber14/tip3p.xml")

potentials = ff.createPotential(prmtop.topology, nonbondedMethod=app.NoCutoff, useDispersionCorrection=False)
params = ff.getParameters()
positions = jnp.array(inpcrd.getPositions(asNumpy=True).value_in_unit(unit.nanometer))

box = jnp.array([[100.0, 0.0, 0.0], [0.0, 100.0, 0.0], [0.0, 0.0, 100.0]])

nbList = NeighborListFreud(box, 20.0, potentials.meta["cov_map"])
nbList.allocate(positions)
pairs = nbList.pairs
efunc = potentials.getPotentialFunc()
dmff_e = efunc(positions, box, pairs, ff.paramset)
print("DMFF Pot E: ", dmff_e)

system = prmtop.createSystem(nonbondedMethod=app.NoCutoff, constraints=None)
integrator = mm.VerletIntegrator(0.001*unit.picoseconds)
platform = mm.Platform.getPlatformByName('Reference')
simulation = app.Simulation(prmtop.topology, system, integrator, platform)
simulation.context.setPositions(inpcrd.positions)

state = simulation.context.getState(getEnergy=True, getVelocities=True, getForces=True, getPositions=True)
energy = state.getPotentialEnergy()
print("OpenMM Pot E: ", energy)

DMFF Pot E:  -6487.265980775686
Initial Pot E:  -6487.229977725502 kJ/mol