import molsysmt as msm
from molsysmt import pyunitwizard as puw
import numpy as np

import openmm as mm
from openmm import app
from openmm import unit

#import os
#from sys import stdout
#from mdtraj.reporters import HDF5Reporter
#from pathlib import Path
#import shutil

modeller = msm.convert(msm.systems['Trp-Cage']['1l2y.h5msm'], to_form='openmm.Modeller', structure_indices=0)
forcefield = app.ForceField("amber14-all.xml", "amber14/tip3p.xml")
system = forcefield.createSystem(modeller.topology, nonbondedMethod=app.NoCutoff, constraints=app.HBonds)
integrator = mm.LangevinIntegrator(300*unit.kelvin, 1.0/unit.picosecond, 2.0*unit.femtoseconds)
platform = mm.Platform.getPlatformByName('CPU')
simulation = app.Simulation(modeller.topology, system, integrator, platform)
simulation.context.setPositions(modeller.positions)
simulation.minimizeEnergy()
simulation.context.setVelocitiesToTemperature(300*unit.kelvin)

tqdm_reporter = msm.thirds.openmm.reporters.TQDMReporter(100,1000)

simulation.reporters.append(tqdm_reporter)

simulation.step(1000)

Potential energy: -1455.63 kJ/mol ± 235.35 kJ/mol
Temperature: 240.44 K ± 30.59 K

Execution time: 0 days, 0 hours, 0 minutes, and 9.19 seconds (18.802 ns/day).

tqdm_reporter._iters

11

tqdm_reporter._end_md_time

2.0000000000000013 ps