diff --git a/molsysmt/_private/digestion/argument/file.py b/molsysmt/_private/digestion/argument/file.py
new file mode 100644
index 000000000..b5e3b8ff4
--- /dev/null
+++ b/molsysmt/_private/digestion/argument/file.py
@@ -0,0 +1,26 @@
+from ...exceptions import ArgumentError
+
+def digest_file(file, caller=None):
+
+    if caller.endswith('write_topology_in_msmh5'):
+
+        from h5py._hl.files import File as h5py_File
+        from molsysmt.native import MSMH5FileHandler
+
+        if isinstance(file, h5py_File):
+            if 'type' in file.attrs:
+                return file
+
+        elif isinstance(file, MSMH5FileHandler):
+                return file
+
+        else:
+
+            from molsysmt.form.file_msmh5.is_form import is_form as is_file_msmh5_form
+            file_is_msmh5 = is_file_msmh5_form(file)
+            if file_is_msmh5:
+                return file
+
+
+    raise ArgumentError('file', value=file, caller=caller, message=None)
+
diff --git a/molsysmt/form/openmm_Simulation/__init__.py b/molsysmt/form/openmm_Simulation/__init__.py
index 6b1014ace..5d5229ab1 100644
--- a/molsysmt/form/openmm_Simulation/__init__.py
+++ b/molsysmt/form/openmm_Simulation/__init__.py
@@ -17,6 +17,7 @@
 from .iterators import StructuresIterator, TopologyIterator
 
 from .to_file_pdb import to_file_pdb
+from .to_file_msmpk import to_file_msmpk
 from .to_molsysmt_Topology import to_molsysmt_Topology
 from .to_openmm_Context import to_openmm_Context
 from .to_openmm_Topology import to_openmm_Topology
@@ -28,6 +29,7 @@
 _convert_to={
         'openmm.Simulation': extract,
         'file:pdb': to_file_pdb,
+        'file:msmpk': to_file_msmpk,
         'molsysmt.Topology': to_molsysmt_Topology,
         'openmm.Context': to_openmm_Context,
         'openmm.Topology': to_openmm_Topology,
diff --git a/molsysmt/form/openmm_Simulation/is_form.py b/molsysmt/form/openmm_Simulation/is_form.py
index 95284fcfa..464a8b193 100644
--- a/molsysmt/form/openmm_Simulation/is_form.py
+++ b/molsysmt/form/openmm_Simulation/is_form.py
@@ -1,6 +1,6 @@
 def is_form(item):
 
-    item_fullname = item.__class__.__module__+'.'+item.__class__.__name__
+    from openmm.app.simulation import Simulation
 
-    return 'openmm.Simulation'==item_fullname
+    return isinstance(item, Simulation)
 
diff --git a/molsysmt/form/openmm_Simulation/to_file_msmpk.py b/molsysmt/form/openmm_Simulation/to_file_msmpk.py
new file mode 100644
index 000000000..6857c1a73
--- /dev/null
+++ b/molsysmt/form/openmm_Simulation/to_file_msmpk.py
@@ -0,0 +1,15 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='openmm.Simulation')
+def to_file_msmpk(item, atom_indices='all', structure_indices='all', output_filename=None):
+
+    from . import to_molsysmt_MolSys as openmm_Simulation_to_molsysmt_MolSys
+    from ..molsysmt_MolSys import to_file_msmpk as molsysmt_MolSys_to_file_msmpk
+
+    tmp_item = openmm_Simulation_to_molsysmt_MolSys(item, atom_indices=atom_indices,
+            structure_indices=structure_indices)
+
+    tmp_item = molsysmt_MolSys_to_file_msmpk(tmp_item, output_filename=output_filename)
+
+    return tmp_item
+
diff --git a/molsysmt/form/openmm_Simulation/to_molsysmt_MolSys.py b/molsysmt/form/openmm_Simulation/to_molsysmt_MolSys.py
index 500508a0a..1fd4b5140 100644
--- a/molsysmt/form/openmm_Simulation/to_molsysmt_MolSys.py
+++ b/molsysmt/form/openmm_Simulation/to_molsysmt_MolSys.py
@@ -9,7 +9,7 @@ def to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all'):
 
     tmp_item = MolSys()
     tmp_item.topology = openmm_Simulation_to_molsysmt_Topology(item, atom_indices=atom_indices)
-    tmp_item.trajectory = openmm_Simulation_to_molsysmt_Structures(item, atom_indices=atom_indices, structure_indices=structure_indices)
+    tmp_item.structures = openmm_Simulation_to_molsysmt_Structures(item, atom_indices=atom_indices, structure_indices=structure_indices)
 
     return tmp_item
 
diff --git a/molsysmt/form/openmm_Simulation/to_openmm_Topology.py b/molsysmt/form/openmm_Simulation/to_openmm_Topology.py
index d15356f46..d081a7c1a 100644
--- a/molsysmt/form/openmm_Simulation/to_openmm_Topology.py
+++ b/molsysmt/form/openmm_Simulation/to_openmm_Topology.py
@@ -3,7 +3,7 @@
 @digest(form='openmm.Simulation')
 def to_openmm_Topology(item, atom_indices='all'):
 
-    from molsysmt.form.openmm_Topology import extract_openmm_Topology
+    from molsysmt.form.openmm_Topology import extract as extract_openmm_Topology
 
     tmp_item = item.topology
     tmp_item = extract_openmm_Topology(tmp_item, atom_indices=atom_indices)
diff --git a/molsysmt/form/openmm_Topology/__init__.py b/molsysmt/form/openmm_Topology/__init__.py
index 8a480cdc4..9d9694277 100644
--- a/molsysmt/form/openmm_Topology/__init__.py
+++ b/molsysmt/form/openmm_Topology/__init__.py
@@ -16,10 +16,11 @@
 from .set import *
 from .iterators import TopologyIterator
 
+from .write_topology_in_msmh5 import write_topology_in_msmh5
+
 from .to_string_pdb_text import to_string_pdb_text
 from .to_file_pdb import to_file_pdb
 from .to_file_psf import to_file_psf
-from .to_file_msmh5 import to_file_msmh5
 from .to_molsysmt_MolSys import to_molsysmt_MolSys
 from .to_molsysmt_Topology import to_molsysmt_Topology
 from .to_mdtraj_Topology import to_mdtraj_Topology
@@ -39,7 +40,6 @@
         'string:pdb_text': to_string_pdb_text,
         'file:pdb': to_file_pdb,
         'file:psf': to_file_psf,
-        'file:msmh5': to_file_msmh5,
         'molsysmt.MolSys': to_molsysmt_MolSys,
         'molsysmt.Topology': to_molsysmt_Topology,
         'mdtraj.Topology': to_mdtraj_Topology,
diff --git a/molsysmt/form/openmm_Topology/to_file_msmh5.py b/molsysmt/form/openmm_Topology/to_file_msmh5.py
deleted file mode 100644
index ab027097c..000000000
--- a/molsysmt/form/openmm_Topology/to_file_msmh5.py
+++ /dev/null
@@ -1,26 +0,0 @@
-from molsysmt._private.digestion import digest
-import h5py
-
-@digest(form='openmm.Topology')
-def to_file_msmh5(item, atom_indices='all', coordinates=None, output_filename=None):
-
-    from molsysmt.native.file_msmh5 import version as msmh5_version
-
-    fff = h5py.File(output_filename, "w")
-
-    fff.attrs['version'] = "1.0"
-    fff.attrs['type'] = "msmh5"
-    fff.attrs['creator'] = "molsysmt"
-
-    add_topology_to_msmh5(item, fff, atom_indices=atom_indices, coordinates=coordinates)
-
-    fff.close()
-
-    tmp_item = output_filename
-
-    return tmp_item
-
-@digest(form='openmm.Topology')
-def add_topology_to_msmh5(item, file, atom_indices='all', coordinates=None):
-
-    raise NotImplementedError
diff --git a/molsysmt/form/openmm_Topology/write_topology_in_msmh5.py b/molsysmt/form/openmm_Topology/write_topology_in_msmh5.py
new file mode 100644
index 000000000..e72befcdd
--- /dev/null
+++ b/molsysmt/form/openmm_Topology/write_topology_in_msmh5.py
@@ -0,0 +1,13 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='openmm.Topology')
+def write_topology_in_msmh5(item, file, atom_indices='all'):
+
+    from . import to_molsysmt_Topology as openmm_Topology_to_molsysmt_Topology
+    from ..molsysmt_Topology import write_topology_in_msmh5 as write_molsysmt_Topology_in_msmh5
+
+    molsysmt_Topology = openmm_Topology_to_molsysmt_Topology(item, atom_indices=atom_indices)
+    write_molsysmt_Topology_in_msmh5(molsysmt_Topology, file)
+
+    pass
+
diff --git a/molsysmt/native/msmh5_file_handler.py b/molsysmt/native/msmh5_file_handler.py
index 7eb5cde29..ee0934b4e 100644
--- a/molsysmt/native/msmh5_file_handler.py
+++ b/molsysmt/native/msmh5_file_handler.py
@@ -31,10 +31,11 @@ def __init__(self, filename, io_mode='r', creator='MolSysMT', compression="gzip"
         if closed:
             self.file.close()
 
-    def write_topology(topology, selection='all', syntax='MolSysMT'):
+    def write_topology(self, topology, selection='all', syntax='MolSysMT'):
 
         from molsysmt.basic import get_form, select, convert
         from molsysmt._private.variables import is_all
+        from molsysmt.form import _dict_modules
 
         if is_all(selection):
             atom_indices = 'all'
@@ -43,11 +44,11 @@ def write_topology(topology, selection='all', syntax='MolSysMT'):
 
         try:
             topology_form = get_form(topology)
-            _dict_modules[topology_form].write_topology_in_msmh5(topology, self.file,
+            _dict_modules[topology_form].write_topology_in_msmh5(topology, file=self.file,
                     atom_indices=atom_indices)
         except:
             aux_topology = convert(topology, to_form='molsysmt.Topology', selection=atom_indices)
-            _dict_modules['molsysmt.Topology'].write_topology_in_msmh5(aux_topology, self.file,
+            _dict_modules['molsysmt.Topology'].write_topology_in_msmh5(aux_topology, file=self.file,
                     atom_indices=atom_indices)
             del(aux_topology)
 
@@ -73,38 +74,36 @@ def _new_msmfile(filename, creator='MolSysMT', compression="gzip", compression_o
     file.attrs['int_precision'] = int_precision
     file.attrs['float_precision'] = int_precision
 
-    structures_sd=file['structures']
-
     if length_unit is None:
-        structures_sd.attrs['length_unit']=puw.get_standard_units(dimensionality={'[L]':1}, form='string')
+        file.attrs['length_unit']=puw.get_standard_units(dimensionality={'[L]':1}, form='string')
     else:
-        structures_sd.attrs['length_unit']=puw.get_unit(length_unit, to_form='string')
+        file.attrs['length_unit']=puw.get_unit(length_unit, to_form='string')
 
     if time_unit is None:
-        structures_sd.attrs['time_unit']=puw.get_standard_units(dimensionality={'[T]':1}, form='string')
+        file.attrs['time_unit']=puw.get_standard_units(dimensionality={'[T]':1}, form='string')
     else:
-        structures_sd.attrs['time_unit']=puw.get_unit(time_unit, to_form='string')
+        file.attrs['time_unit']=puw.get_unit(time_unit, to_form='string')
 
     if energy_unit is None:
-        structures_sd.attrs['energy_unit']=puw.get_standard_units(dimensionality={'[L]':2, '[M]':1,
+        file.attrs['energy_unit']=puw.get_standard_units(dimensionality={'[L]':2, '[M]':1,
             '[T]':-2, '[mol]':-1}, form='string')
     else:
-        structures_sd.attrs['energy_unit']=puw.get_unit(energy_unit, to_form='string')
+        file.attrs['energy_unit']=puw.get_unit(energy_unit, to_form='string')
 
     if temperature_unit is None:
-        structures_sd.attrs['temperature_unit']=puw.get_standard_units(dimensionality={'[K]':1}, form='string')
+        file.attrs['temperature_unit']=puw.get_standard_units(dimensionality={'[K]':1}, form='string')
     else:
-        structures_sd.attrs['temperature_unit']=puw.get_unit(temperature_unit, to_form='string')
+        file.attrs['temperature_unit']=puw.get_unit(temperature_unit, to_form='string')
 
     if temperature_unit is None:
-        structures_sd.attrs['charge_unit']=puw.get_standard_units(dimensionality={'[A]':1, '[T]':1}, form='string')
+        file.attrs['charge_unit']=puw.get_standard_units(dimensionality={'[A]':1, '[T]':1}, form='string')
     else:
-        structures_sd.attrs['charge_unit']=puw.get_unit(temperature_unit, to_form='string')
+        file.attrs['charge_unit']=puw.get_unit(temperature_unit, to_form='string')
 
     if temperature_unit is None:
-        structures_sd.attrs['mass_unit']=puw.get_standard_units(dimensionality={'[M]':1}, form='string')
+        file.attrs['mass_unit']=puw.get_standard_units(dimensionality={'[M]':1}, form='string')
     else:
-        structures_sd.attrs['mass_unit']=puw.get_unit(mass_unit, to_form='string')
+        file.attrs['mass_unit']=puw.get_unit(mass_unit, to_form='string')
 
     global_dataset_options = {
             'compression':compression,
@@ -193,15 +192,16 @@ def _new_msmfile(filename, creator='MolSysMT', compression="gzip", compression_o
 
     # Structures
 
-    structures_sd = file.create_group("structures_sd")
+    structures_sd = file.create_group("structures")
     structures_sd.attrs['n_atoms'] = 0
-    structures_sd.attrs['n_structures_sd'] = 0
-    structures_sd.attrs['n_structures_sd_to_be_written'] = 0
+    structures_sd.attrs['n_structures'] = 0
+    structures_sd.attrs['n_structures_written'] = 0
     structures_sd.attrs['constant_time_step']=False
     structures_sd.attrs['time_step']=0.0
     structures_sd.attrs['constant_id_step']=False
     structures_sd.attrs['id_step']=0
     structures_sd.attrs['constant_box']=False
+    structures_sd.attrs['pbc']='pbc' # none, cell, mic, continuous
 
     structures_sd.create_dataset('id', (0,), dtype=int_type, maxshape=(None,), **global_dataset_options)
     structures_sd.create_dataset('time', (0,), dtype=float_type, maxshape=(None,), **global_dataset_options)
diff --git a/molsysmt/thirds/openmm/reporters/msmh5.py b/molsysmt/thirds/openmm/reporters/msmh5.py
index 4488ce1c5..185c379cf 100644
--- a/molsysmt/thirds/openmm/reporters/msmh5.py
+++ b/molsysmt/thirds/openmm/reporters/msmh5.py
@@ -1,14 +1,16 @@
 from molsysmt._private.variables import is_all
 import numpy as np
+import openmm as mm
+from openmm import unit
 
 class MSMH5Reporter(object):
 
-    def __init__(self, file, reportInterval, selection='all', steps=None,
+    def __init__(self, file, reportInterval, steps, selection='all',
             topology=True, time=True, box=True, coordinates=True, velocities=False,
             potentialEnergy=False, kineticEnergy=False, temperature=False,
             includeInitialContext=True, constantReportInterval=True,
             constantStepSize=True, constantBox=True,
-            compression='gzip', compression_opts=4,
+            compression='lzf', compression_opts=None,
             int_precision='single', float_precision='single',
             syntax='MolSysMT'):
 
@@ -45,8 +47,7 @@ def __init__(self, file, reportInterval, selection='all', steps=None,
         self._selection_is_all = False
         self._syntax = syntax
 
-        self._n_intervals_to_be_reported = None
-        self._n_intervals_reported = 0
+        self._n_structures_reported = 0
 
         self._file_handler = MSMH5FileHandler(file, io_mode='w', creator='OpenMM',
                 compression=compression, compression_opts=compression_opts,
@@ -59,7 +60,6 @@ def __init__(self, file, reportInterval, selection='all', steps=None,
     def _initialize(self, simulation):
 
         from molsysmt.basic import select, get
-        import openmm as mm
 
         system = simulation.system
         context = simulation.context
@@ -68,6 +68,7 @@ def _initialize(self, simulation):
 
         if not is_all(self._selection):
             self._selection = select(topology, selection=self._selection, syntax=self._syntax)
+            self._selection_is_all = False
             self._n_atoms = len(self._selection)
         else:
             self._selection_is_all = True
@@ -81,7 +82,7 @@ def _initialize(self, simulation):
         if self._temperature:
             dof = 0
             for i in range(system.getNumParticles()):
-                if system.getParticleMass(i) > 0*unit.dalton:
+                if system.getParticleMass(i) > 0.0*unit.dalton:
                     dof += 3
             dof -= system.getNumConstraints()
             if any(isinstance(frc, mm.CMMotionRemover) for frc in frclist):
@@ -92,53 +93,53 @@ def _initialize(self, simulation):
             if system.usesPeriodicBoundaryConditions():
                 if  self._constant_box:
                     self._constant_box = True # Barostat needs to be checked
-                    self._structures_sd.attr['constant_box']=True
+                    self._structures_sd.attrs['constant_box']=True
 
         if self._constant_report_interval:
-            self._structures_sd.attr['constant_id_step']=True
+            self._structures_sd.attrs['constant_id_step']=True
             if self._constant_step_size:
                 self._step_size = integrator.getStepSize()
-                self._structures_sd.attr['constant_time_step']=True
+                self._structures_sd.attrs['constant_time_step']=True
 
         if self._steps is not None:
 
-            self.n_intervals_to_be_reported = int(self._steps/self._report_interval)
+            self._steps = int(self._steps/self._report_interval)
             if self._include_initial_context:
-                self.n_intervals_to_be_reported +=1
+                self._steps +=1
 
             if self._constant_report_interval:
-                self._structures_sd['id'].resize((1))
+                self._structures_sd['id'].resize((1,))
             else:
-                self._structures_sd['id'].resize((n_intervals_to_be_reported))
+                self._structures_sd['id'].resize((self._steps))
 
             if self._time:
                 if self._constant_report_interval and self._constant_step_size:
-                    self._structures_sd['time'].resize((1))
+                    self._structures_sd['time'].resize((1,))
                 else:
-                    self._structures_sd['time'].resize((n_intervals_to_be_reported))
+                    self._structures_sd['time'].resize((self._steps))
 
             if self._box:
                 if self._constant_box:
                     self._structures_sd['box'].resize((1, 3, 3))
                 else:
-                    self._structures_sd['box'].resize((n_intervals_to_be_reported, 3, 3))
+                    self._structures_sd['box'].resize((self._steps, 3, 3))
 
             if self._coordinates:
-                self._structures_sd['coordinates'].resize((n_intervals_to_be_reported, self._n_atoms, 3))
+                self._structures_sd['coordinates'].resize((self._steps, self._n_atoms, 3))
 
             if self._velocities:
-                self._structures_sd['velocities'].resize((n_intervals_to_be_reported, self._n_atoms, 3))
+                self._structures_sd['velocities'].resize((self._steps, self._n_atoms, 3))
 
             if self._kinetic_energy:
-                self._structures_sd['kinetic_energy'].resize((n_intervals_to_be_reported))
+                self._structures_sd['kinetic_energy'].resize((self._steps,))
 
             if self._potential_energy:
-                self._structures_sd['potential_energy'].resize((n_intervals_to_be_reported))
+                self._structures_sd['potential_energy'].resize((self._steps,))
 
             if self._temperature:
-                self._structures_sd['temperature'].resize((n_intervals_to_be_reported))
+                self._structures_sd['temperature'].resize((self._steps,))
 
-            self._structures_sd.attrs['n_structures_to_be_written'] = self._n_intervals_to_be_reported
+            self._structures_sd.attrs['n_structures'] = self._steps
 
         if self._include_initial_context:
             initial_state = simulation.context.getState(getPositions=self._needs_positions,
@@ -152,13 +153,17 @@ def _initialize(self, simulation):
 
     def describeNextReport(self, simulation):
 
-        steps_left = simulation.currentStep % self._reportInterval
-        steps = self._reportInterval - steps_left
-        return (steps, self._needsPositions, self._needsVelocities, self._needsForces, self._needEnergy)
+        if not self._initialized:
+            self._initialize(simulation)
+
+        steps_left = simulation.currentStep % self._report_interval
+        steps = self._report_interval - steps_left
+        return (steps, self._needs_positions, self._needs_velocities, self._needs_forces,
+                self._needs_energy)
 
     def report(self, simulation, state):
 
-        index = self._n_intervals_reported
+        index = self._n_structures_reported
 
         if self._id:
             self._structures_sd['id'][index] = simulation.currentStep
@@ -199,8 +204,8 @@ def report(self, simulation, state):
             self._structures_sd['temperature'][index] = temperature._value
 
 
-        self._n_intervals_reported += 1
-        self._structures_sd.attrs['n_structures'] = self._n_intervals_reported
+        self._n_structures_reported += 1
+        self._structures_sd.attrs['n_structures_written'] = self._n_structures_reported
 
         pass
 
diff --git a/sandbox/Test-Copy1.ipynb b/sandbox/Test-Copy1.ipynb
new file mode 100644
index 000000000..1640458fa
--- /dev/null
+++ b/sandbox/Test-Copy1.ipynb
@@ -0,0 +1,285 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "85d75849-5640-43b7-8b93-87cdbf6b8792",
+   "metadata": {},
+   "source": [
+    "# Test2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "08aee8bc-0efe-44a5-9aa6-24131ae8137e",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "f9f8114975664ee5820dc4159d40d228",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "import molsysmt as msm"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "4ad7bc96-0f77-4bb5-bfa0-fa5296ed5d3d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import openmm as mm\n",
+    "from openmm import app\n",
+    "from openmm import unit"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "4d812609-a0d8-462f-844d-58fb5fd20044",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "molsys = msm.convert('initial.msmpk')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "f8c8da61-9fcd-464e-8527-cc07294a3f59",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "topology = msm.convert(molsys, 'openmm.Topology')\n",
+    "coordinates = msm.get(molsys, coordinates=True)\n",
+    "positions = msm.pyunitwizard.convert(coordinates[0], to_form='openmm.unit')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "faf46e30-3984-462d-b82a-67fa375d0dad",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "forcefield = app.ForceField('amber14-all.xml', 'amber14/tip3p.xml')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "a64d8439-6611-4129-9a4d-993cbf83ce67",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "system = forcefield.createSystem(topology, nonbondedMethod=app.PME,\n",
+    "        nonbondedCutoff=1.2*unit.nanometer, constraints=app.HBonds)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "fc909c3f-345d-4c1f-b5f8-eb71eb22bf76",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "integrator = mm.LangevinIntegrator(300*unit.kelvin, 1.0/unit.picosecond, 2.0*unit.femtoseconds)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "a722c9e4-cfca-43f8-8710-1c028aea6569",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "platform = mm.Platform.getPlatformByName(\"CPU\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "4102c0c6-7d97-4964-bbe9-f24356e97b08",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "simulation = app.Simulation(topology, system, integrator, platform)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ec61ac73-777e-4d22-b3d7-cbc32b4a8cac",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "simulation.context.setPositions(positions)\n",
+    "#simulation.minimizeEnergy()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "20516706-23cc-476e-b330-b7bd22b88ef3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.convert(simulation, 'initial.msmpk')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "00d2a551-dd8e-4678-9e48-aa8a4765664e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "aa = msm.convert(simulation)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2aa4de52-b0fe-4bb4-9f21-5ccef4075d04",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.info(aa)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "21c83228-ba57-450b-967b-b7b6195e2a1a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#from molsysmt.thirds.openmm.reporters import MolSysMTTrajectoryDictReporter\n",
+    "#from molsysmt.thirds.openmm.reporters import MSMH5Reporter\n",
+    "#from mdtraj.reporters import HDF5Reporter\n",
+    "from molsysmt.thirds.openmm.reporters import TQDMReporter"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7282a59c-8f33-45e9-914d-878659a93cac",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#dict_reporter = MolSysMTTrajectoryDictReporter(10)\n",
+    "#simulation.reporters.append(dict_reporter)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "044d948f-1d5f-4f43-b4ca-eac0a29235a9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#msmh5_reporter = MSMH5Reporter('test.msmh5', 100, steps=100, selection='all',\n",
+    "#            topology=True, time=True, box=True, coordinates=True, velocities=False,\n",
+    "#            potentialEnergy=True, kineticEnergy=True, temperature=True,\n",
+    "#            includeInitialContext=True, constantReportInterval=True,\n",
+    "#            constantStepSize=True, constantBox=True,\n",
+    "#            compression='gzip', compression_opts=4,\n",
+    "#            int_precision='single', float_precision='single',\n",
+    "#            syntax='MolSysMT')\n",
+    "#simulation.reporters.append(msmh5_reporter)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6e6dac3f-1ba1-4cb4-ba4d-e11067da6a77",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#h5_reporter = HDF5Reporter('test2.msmh5', 10)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "330346e6-fd22-4fb6-b37e-e399d5c4b054",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%time\n",
+    "simulation.step(5000)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "69ad2b4f-0c98-4e01-9e4c-73ba0a00ff85",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "h5_reporter.close()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "698f41f6-803c-4865-a581-40fc5bbb4dd2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "traj = dict_reporter.finalize()\n",
+    "msmh5_reporter.close()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4e0f2b4c-4248-4555-ba73-ad3cf315fb89",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "614409f6-4201-4c10-8983-c722e52a76ee",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "CPU times: user 53.2 s, sys: 382 ms, total: 53.6 s\n",
+    "Wall time: 3.12 s"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/sandbox/Test.ipynb b/sandbox/Test.ipynb
index 18de4ceb9..86d0e9836 100644
--- a/sandbox/Test.ipynb
+++ b/sandbox/Test.ipynb
@@ -17,7 +17,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "4d9fc4c0fdd449079c0fed4e538f3275",
+       "model_id": "bb10351d0a0548a698881062f85ee8e4",
        "version_major": 2,
        "version_minor": 0
       },
@@ -50,147 +50,154 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "molsys = msm.convert('4POC')"
+    "#molsys = msm.convert('4POC')\n",
+    "#molsys = msm.extract(molsys, selection='molecule_type==\"protein\"')\n",
+    "#molsys = msm.build.add_missing_hydrogens(molsys)\n",
+    "#molsys = msm.build.solvate(molsys)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "046c5eec-7ab2-409c-9291-da9c19e67728",
+   "id": "af701dd9-f4c2-4731-93c4-29eaea41fd06",
    "metadata": {},
    "outputs": [],
    "source": [
-    "molsys = msm.extract(molsys, selection='molecule_type==\"protein\"')"
+    "molsys = msm.convert('initial.msmpk')"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 5,
-   "id": "72ecea0d-a32d-49da-b929-2ceb66136b8e",
+   "id": "8ae23b96-3d4b-425a-af14-34db7e2b6edc",
    "metadata": {},
    "outputs": [],
    "source": [
-    "molsys = msm.build.add_missing_hydrogens(molsys)"
+    "topology = msm.convert(molsys, 'openmm.Topology')\n",
+    "coordinates = msm.get(molsys, coordinates=True)\n",
+    "positions = msm.pyunitwizard.convert(coordinates[0], to_form='openmm.unit')"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 6,
-   "id": "5b5471e7-546b-40fc-8bae-e4efd798a3fc",
+   "id": "faf46e30-3984-462d-b82a-67fa375d0dad",
    "metadata": {},
    "outputs": [],
    "source": [
-    "molsys = msm.build.solvate(molsys)"
+    "forcefield = app.ForceField('amber14-all.xml', 'amber14/tip3p.xml')"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 7,
-   "id": "faf46e30-3984-462d-b82a-67fa375d0dad",
+   "id": "a64d8439-6611-4129-9a4d-993cbf83ce67",
    "metadata": {},
    "outputs": [],
    "source": [
-    "forcefield = app.ForceField('amber14-all.xml', 'amber14/tip3p.xml')"
+    "system = forcefield.createSystem(topology, nonbondedMethod=app.PME,\n",
+    "        nonbondedCutoff=1.2*unit.nanometer, constraints=app.HBonds)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 8,
-   "id": "610249ba-1992-4457-aa75-90f8ec791d9c",
+   "id": "fc909c3f-345d-4c1f-b5f8-eb71eb22bf76",
    "metadata": {},
    "outputs": [],
    "source": [
-    "topology = msm.convert(molsys, 'openmm.Topology')"
+    "integrator = mm.LangevinIntegrator(300*unit.kelvin, 1.0/unit.picosecond, 2.0*unit.femtoseconds)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 9,
-   "id": "a64d8439-6611-4129-9a4d-993cbf83ce67",
+   "id": "a722c9e4-cfca-43f8-8710-1c028aea6569",
    "metadata": {},
    "outputs": [],
    "source": [
-    "system = forcefield.createSystem(topology, nonbondedMethod=app.PME,\n",
-    "        nonbondedCutoff=1.2*unit.nanometer, constraints=app.HBonds)"
+    "platform = mm.Platform.getPlatformByName(\"CPU\")"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 10,
-   "id": "fc909c3f-345d-4c1f-b5f8-eb71eb22bf76",
+   "id": "4102c0c6-7d97-4964-bbe9-f24356e97b08",
    "metadata": {},
    "outputs": [],
    "source": [
-    "integrator = mm.LangevinIntegrator(300*unit.kelvin, 1.0/unit.picosecond, 2.0*unit.femtoseconds)"
+    "simulation = app.Simulation(topology, system, integrator, platform)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 11,
-   "id": "a722c9e4-cfca-43f8-8710-1c028aea6569",
+   "id": "ec61ac73-777e-4d22-b3d7-cbc32b4a8cac",
    "metadata": {},
    "outputs": [],
    "source": [
-    "platform = mm.Platform.getPlatformByName(\"CPU\")"
+    "simulation.context.setPositions(positions)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 12,
-   "id": "4102c0c6-7d97-4964-bbe9-f24356e97b08",
+   "id": "20516706-23cc-476e-b330-b7bd22b88ef3",
    "metadata": {},
    "outputs": [],
    "source": [
-    "simulation = app.Simulation(topology, system, integrator, platform)"
+    "#simulation.minimizeEnergy()\n",
+    "#msm.convert(simulation, 'initial.msmpk')"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 13,
-   "id": "b3cbdb1e-1eb1-430e-be46-7b20a9e3928e",
+   "id": "21c83228-ba57-450b-967b-b7b6195e2a1a",
    "metadata": {},
    "outputs": [],
    "source": [
-    "coordinates = msm.get(molsys, coordinates=True)\n",
-    "positions = msm.pyunitwizard.convert(coordinates[0], to_form='openmm.unit')"
+    "#from molsysmt.thirds.openmm.reporters import MolSysMTTrajectoryDictReporter\n",
+    "from molsysmt.thirds.openmm.reporters import MSMH5Reporter\n",
+    "from mdtraj.reporters import HDF5Reporter\n",
+    "from molsysmt.thirds.openmm.reporters import TQDMReporter"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 14,
-   "id": "ec61ac73-777e-4d22-b3d7-cbc32b4a8cac",
+   "id": "1561ddce-b2b2-4d7a-911d-c05a92cd0fa4",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "7a2e3a3a37a546718ea50a67d4181e25",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "  0%|          | 0/5000 [00:00<?, ?it/s]"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
-    "simulation.context.setPositions(positions)\n",
-    "simulation.minimizeEnergy()"
+    "tqdm_reporter = TQDMReporter(100, 5000)\n",
+    "simulation.reporters.append(tqdm_reporter)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "20516706-23cc-476e-b330-b7bd22b88ef3",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "00d2a551-dd8e-4678-9e48-aa8a4765664e",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": 15,
-   "id": "21c83228-ba57-450b-967b-b7b6195e2a1a",
+   "id": "6e6dac3f-1ba1-4cb4-ba4d-e11067da6a77",
    "metadata": {},
    "outputs": [],
    "source": [
-    "from molsysmt.thirds.openmm.reporters import MolSysMTTrajectoryDictReporter\n",
-    "from molsysmt.thirds.openmm.reporters import MSMH5Reporter"
+    "#h5_reporter = HDF5Reporter('test.h5', 100)\n",
+    "#simulation.reporters.append(h5_reporter)"
    ]
   },
   {
@@ -200,8 +207,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dict_reporter = MolSysMTTrajectoryDictReporter(10)\n",
-    "simulation.reporters.append(dict_reporter)"
+    "#dict_reporter = MolSysMTTrajectoryDictReporter(10)\n",
+    "#simulation.reporters.append(dict_reporter)"
    ]
   },
   {
@@ -209,48 +216,54 @@
    "execution_count": 17,
    "id": "044d948f-1d5f-4f43-b4ca-eac0a29235a9",
    "metadata": {},
+   "outputs": [],
+   "source": [
+    "msmh5_reporter = MSMH5Reporter('test.msmh5', 100, steps=5000, selection='all',\n",
+    "            topology=True, time=True, box=True, coordinates=True, velocities=False,\n",
+    "            potentialEnergy=True, kineticEnergy=True, temperature=True,\n",
+    "            includeInitialContext=True, constantReportInterval=True,\n",
+    "            constantStepSize=True, constantBox=True)\n",
+    "simulation.reporters.append(msmh5_reporter)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "id": "330346e6-fd22-4fb6-b37e-e399d5c4b054",
+   "metadata": {},
    "outputs": [
     {
-     "ename": "KeyError",
-     "evalue": "\"Unable to synchronously open object (object 'structures' doesn't exist)\"",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[17], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m msmh5_reporter \u001b[38;5;241m=\u001b[39m \u001b[43mMSMH5Reporter\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mtest.msmh5\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m10\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mselection\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mall\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msteps\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m100\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m      2\u001b[0m \u001b[43m            \u001b[49m\u001b[43mtopology\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtime\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mbox\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcoordinates\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mvelocities\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m      3\u001b[0m \u001b[43m            \u001b[49m\u001b[43mpotentialEnergy\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mkineticEnergy\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtemperature\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m      4\u001b[0m \u001b[43m            \u001b[49m\u001b[43mincludeInitialContext\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mconstantReportInterval\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m      5\u001b[0m \u001b[43m            \u001b[49m\u001b[43mconstantStepSize\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mconstantBox\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m      6\u001b[0m \u001b[43m            \u001b[49m\u001b[43mcompression\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mgzip\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcompression_opts\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m4\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m      7\u001b[0m \u001b[43m            \u001b[49m\u001b[43mint_precision\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43msingle\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfloat_precision\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43msingle\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m      8\u001b[0m \u001b[43m            \u001b[49m\u001b[43msyntax\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mMolSysMT\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m      9\u001b[0m simulation\u001b[38;5;241m.\u001b[39mreporters\u001b[38;5;241m.\u001b[39mappend(msmh5_reporter)\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/thirds/openmm/reporters/msmh5.py:51\u001b[0m, in \u001b[0;36mMSMH5Reporter.__init__\u001b[0;34m(self, file, reportInterval, selection, steps, topology, time, box, coordinates, velocities, potentialEnergy, kineticEnergy, temperature, includeInitialContext, constantReportInterval, constantStepSize, constantBox, compression, compression_opts, int_precision, float_precision, syntax)\u001b[0m\n\u001b[1;32m     48\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_n_intervals_to_be_reported \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m     49\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_n_intervals_reported \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m0\u001b[39m\n\u001b[0;32m---> 51\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_file_handler \u001b[38;5;241m=\u001b[39m \u001b[43mMSMH5FileHandler\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfile\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mio_mode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mw\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcreator\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mOpenMM\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m     52\u001b[0m \u001b[43m        \u001b[49m\u001b[43mcompression\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcompression\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcompression_opts\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcompression_opts\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     53\u001b[0m \u001b[43m        \u001b[49m\u001b[43mint_precision\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mint_precision\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfloat_precision\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfloat_precision\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     54\u001b[0m \u001b[43m        \u001b[49m\u001b[43mlength_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mnm\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtime_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mps\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43menergy_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mkJ/mol\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m     55\u001b[0m \u001b[43m        \u001b[49m\u001b[43mtemperature_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mkelvin\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcharge_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43me\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mmass_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mdalton\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m     57\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_structures_sd \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_file_handler\u001b[38;5;241m.\u001b[39mfile[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mstructures\u001b[39m\u001b[38;5;124m'\u001b[39m]\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/native/msmh5_file_handler.py:17\u001b[0m, in \u001b[0;36mMSMH5FileHandler.__init__\u001b[0;34m(self, filename, io_mode, creator, compression, compression_opts, int_precision, float_precision, length_unit, time_unit, energy_unit, temperature_unit, charge_unit, mass_unit, closed)\u001b[0m\n\u001b[1;32m     13\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfile \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m     15\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m io_mode\u001b[38;5;241m==\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mw\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[0;32m---> 17\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfile \u001b[38;5;241m=\u001b[39m \u001b[43m_new_msmfile\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfilename\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcreator\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcreator\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcompression\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcompression\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     18\u001b[0m \u001b[43m            \u001b[49m\u001b[43mcompression_opts\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcompression_opts\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mint_precision\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mint_precision\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     19\u001b[0m \u001b[43m            \u001b[49m\u001b[43mfloat_precision\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfloat_precision\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mlength_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mlength_unit\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtime_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtime_unit\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     20\u001b[0m \u001b[43m            \u001b[49m\u001b[43menergy_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43menergy_unit\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtemperature_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtemperature_unit\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     21\u001b[0m \u001b[43m            \u001b[49m\u001b[43mcharge_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcharge_unit\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mmass_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmass_unit\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     23\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m io_mode\u001b[38;5;241m==\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mr\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[1;32m     25\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfile \u001b[38;5;241m=\u001b[39m h5py\u001b[38;5;241m.\u001b[39mFile(filename, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mr\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n",
-      "File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/native/msmh5_file_handler.py:76\u001b[0m, in \u001b[0;36m_new_msmfile\u001b[0;34m(filename, creator, compression, compression_opts, int_precision, float_precision, length_unit, time_unit, energy_unit, temperature_unit, charge_unit, mass_unit)\u001b[0m\n\u001b[1;32m     73\u001b[0m file\u001b[38;5;241m.\u001b[39mattrs[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mint_precision\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m int_precision\n\u001b[1;32m     74\u001b[0m file\u001b[38;5;241m.\u001b[39mattrs[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mfloat_precision\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m int_precision\n\u001b[0;32m---> 76\u001b[0m structures_sd\u001b[38;5;241m=\u001b[39m\u001b[43mfile\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mstructures\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m]\u001b[49m\n\u001b[1;32m     78\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m length_unit \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m     79\u001b[0m     structures_sd\u001b[38;5;241m.\u001b[39mattrs[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mlength_unit\u001b[39m\u001b[38;5;124m'\u001b[39m]\u001b[38;5;241m=\u001b[39mpuw\u001b[38;5;241m.\u001b[39mget_standard_units(dimensionality\u001b[38;5;241m=\u001b[39m{\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m[L]\u001b[39m\u001b[38;5;124m'\u001b[39m:\u001b[38;5;241m1\u001b[39m}, form\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mstring\u001b[39m\u001b[38;5;124m'\u001b[39m)\n",
-      "File \u001b[0;32mh5py/_objects.pyx:54\u001b[0m, in \u001b[0;36mh5py._objects.with_phil.wrapper\u001b[0;34m()\u001b[0m\n",
-      "File \u001b[0;32mh5py/_objects.pyx:55\u001b[0m, in \u001b[0;36mh5py._objects.with_phil.wrapper\u001b[0;34m()\u001b[0m\n",
-      "File \u001b[0;32m~/Myopt/miniconda3/envs/MolSysMT@uibcdf_3.10/lib/python3.10/site-packages/h5py/_hl/group.py:357\u001b[0m, in \u001b[0;36mGroup.__getitem__\u001b[0;34m(self, name)\u001b[0m\n\u001b[1;32m    355\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mInvalid HDF5 object reference\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m    356\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(name, (\u001b[38;5;28mbytes\u001b[39m, \u001b[38;5;28mstr\u001b[39m)):\n\u001b[0;32m--> 357\u001b[0m     oid \u001b[38;5;241m=\u001b[39m \u001b[43mh5o\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mid\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_e\u001b[49m\u001b[43m(\u001b[49m\u001b[43mname\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mlapl\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_lapl\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    358\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    359\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mAccessing a group is done with bytes or str, \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m    360\u001b[0m                     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mnot \u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\u001b[38;5;28mtype\u001b[39m(name)))\n",
-      "File \u001b[0;32mh5py/_objects.pyx:54\u001b[0m, in \u001b[0;36mh5py._objects.with_phil.wrapper\u001b[0;34m()\u001b[0m\n",
-      "File \u001b[0;32mh5py/_objects.pyx:55\u001b[0m, in \u001b[0;36mh5py._objects.with_phil.wrapper\u001b[0;34m()\u001b[0m\n",
-      "File \u001b[0;32mh5py/h5o.pyx:190\u001b[0m, in \u001b[0;36mh5py.h5o.open\u001b[0;34m()\u001b[0m\n",
-      "\u001b[0;31mKeyError\u001b[0m: \"Unable to synchronously open object (object 'structures' doesn't exist)\""
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "CPU times: user 47min 57s, sys: 18.4 s, total: 48min 15s\n",
+      "Wall time: 2min 57s\n"
      ]
     }
    ],
    "source": [
-    "msmh5_reporter = MSMH5Reporter('test.msmh5', 10, selection='all', steps=100,\n",
-    "            topology=True, time=True, box=True, coordinates=True, velocities=False,\n",
-    "            potentialEnergy=True, kineticEnergy=True, temperature=True,\n",
-    "            includeInitialContext=True, constantReportInterval=True,\n",
-    "            constantStepSize=True, constantBox=True,\n",
-    "            compression='gzip', compression_opts=4,\n",
-    "            int_precision='single', float_precision='single',\n",
-    "            syntax='MolSysMT')\n",
-    "simulation.reporters.append(msmh5_reporter)"
+    "%%time\n",
+    "simulation.step(5000)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "330346e6-fd22-4fb6-b37e-e399d5c4b054",
+   "id": "69ad2b4f-0c98-4e01-9e4c-73ba0a00ff85",
    "metadata": {},
    "outputs": [],
    "source": [
-    "simulation.step(100)"
+    "h5_reporter.close()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "id": "164e05f5-dd74-4589-a483-da08e4db4561",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msmh5_reporter.close()"
    ]
   },
   {
@@ -267,10 +280,21 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4e0f2b4c-4248-4555-ba73-ad3cf315fb89",
+   "id": "614409f6-4201-4c10-8983-c722e52a76ee",
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "tqdm : 30 it/s\n",
+    "CPU times: user 47min 36s, sys: 18.1 s, total: 47min 54s\n",
+    "Wall time: 2min 45s\n",
+    "\n",
+    "tqdm + h5: 30 it/s\n",
+    "CPU times: user 46min 52s, sys: 17.9 s, total: 47min 10s\n",
+    "Wall time: 2min 44s\n",
+    "\n",
+    "\n",
+    "\n"
+   ]
   }
  ],
  "metadata": {
diff --git a/sandbox/initial.msmpk b/sandbox/initial.msmpk
new file mode 100644
index 000000000..e70e2c45d
Binary files /dev/null and b/sandbox/initial.msmpk differ
diff --git a/sandbox/last_10_frames.h5 b/sandbox/last_10_frames.h5
deleted file mode 100644
index 29c63def7..000000000
Binary files a/sandbox/last_10_frames.h5 and /dev/null differ
diff --git a/sandbox/micro_traj_eq.h5 b/sandbox/micro_traj_eq.h5
deleted file mode 100644
index dfd9325ff..000000000
Binary files a/sandbox/micro_traj_eq.h5 and /dev/null differ
diff --git a/sandbox/test.msmh5 b/sandbox/test.msmh5
deleted file mode 100644
index be0074833..000000000
Binary files a/sandbox/test.msmh5 and /dev/null differ
diff --git a/sandbox/traj.h5 b/sandbox/traj.h5
deleted file mode 100644
index ae3c0138d..000000000
Binary files a/sandbox/traj.h5 and /dev/null differ
diff --git a/sandbox/traj_ions.h5 b/sandbox/traj_ions.h5
deleted file mode 100644
index dd78cc83d..000000000
Binary files a/sandbox/traj_ions.h5 and /dev/null differ
diff --git a/sandbox/traj_ions_peptide.h5 b/sandbox/traj_ions_peptide.h5
deleted file mode 100644
index a3f7993e4..000000000
Binary files a/sandbox/traj_ions_peptide.h5 and /dev/null differ