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OpenFE Showcase: Relative Binding Free Energy of T4 Lysozyme#

1. Overview#

In this example we look how one could set up a network of transformations using the OpenFE toolkit for small chemical modifications of an initial known binder, benzene, to T4-lysozyme L99A.

Crystallographic and affinity data (dG of -5.2 kcal/mol) are available for benzene and demonstrate the ligand to bind within the lipophylic cavity of T4-lysozyme L99A.

image.png

This notebook demonstrates the current capabilities of the OpenFE toolkit. Here we specifically look at how relative binding free energy calculations can be carried out using the OpenMM MD engine in combination with the OpenFE toolset. This notebook will be continually updated as OpenFE introduces new features.

For convenience, a prepared (capped and protonated) PDB structure of the T4-lysozyme L994A protein is provided under inputs/181L_mod_capped_protonated.pdb.

Alchemical transformations of benzene#

Chemical modifications benzene binding to T4 lysozyme are relatively well studied, examples can be seen in the works of Mobley et al. and Gapsys et al.. Here we explore how OpenFE can be used to build a simple star map network for planned alchemical substitutions of the core benzene ring.

Five pre-aligned compounds (phenol, toluene, anisole, styrene, benzonitrile, and benzaldehyde) and the benzene core are available under inputs/ligands.sdf. These are shown in the cell below.

[4]:

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw

# Extract the contents of the sdf file and visualise it
ligands_rdmol = [mol for mol in
                 Chem.SDMolSupplier('inputs/ligands.sdf', removeHs=False)]

for ligand in ligands_rdmol:
    AllChem.Compute2DCoords(ligand)

Chem.Draw.MolsToGridImage(ligands_rdmol)

[4]:
../_images/tutorials_showcase_notebook_6_0.png

Ultimately we will limit the RBFEs done in this notebook to the transformation of benzene to phenol, as similarly done in the AMBER free energy tutorial. Previous work has shown that phenol does not bind to T4-Lysozyme L99A, so we expect that the RBFE will capture the positive change in the free energy.

The plan#

Here is what we will achieve in this notebook and what software toolchains are used along the way.

Actions

Software

Create OpenFE Molecules

OpenFE tk, RDKit

Create Radial Network

OpenFE tk, Lomap, Networkx

Visualise Network

OpenFE tk, NetworkX, RDKit, Matplotlib

Create ligand topologies

OpenFE tk interface - OpenFF tk

Create hybrid OpenMM topology

OpenFE tk interface - OpenMMTools (eventually - ex Perses)

Create Lambda Protocol

OpenFE tk interface - OpenMMTools (eventually - ex Perses)

Setup and run RBFE calculation

OpenFE tk interface - OpenMM + OpenMMTools

Analysis RBFE calculation

OpenFE tk interface - PyMBAR + OpenMMTools

A complete overview of the setup and simulation process starting from initial SDF and PDB files can be found in this diagram.

2. Creating a transformation network#

Creating OpenFE SmallMoleculeComponents#

In order to keep track of the various inputs being passed through the OpenFE toolkit, OpenFE implements a set of Components which define the proteins, small molecules and solvent components which a system may contain. Here we use the SmallMoleculeComponent which takes in either RDKit molecules or OpenFF molecules.

In the backend, OpenFE treats the RDKit molecules as the central representation of the ligands, and uses the OpenFF toolkit to convert between objects from various toolchains (for example OpenEye’s OEMol).

Here we demonstrate how to load the ligands from inputs/ligands.sdf into a list of OpenFE SmallMoleculeComponents for further processing.

[5]:

from openfe import SmallMoleculeComponent

# Create and SDF supplier
# Extract the contents of the sdf file and visualise it
ligands_sdf = Chem.SDMolSupplier('inputs/ligands.sdf', removeHs=False)

# Now pass these to form a list of Molecules
ligand_mols = [SmallMoleculeComponent(sdf) for sdf in ligands_sdf]

OpenFE SmallMoleculeComponents have some useful built in attributes and methods.

For example the molecule’s name (as defined by the SDF file) can be accessed

[6]:

print("name: ", ligand_mols[0].name)

name:  benzene

SmallMoleculeComponents also have a means of serialising through their to_dict() method.

[7]:

ligand_mols[0].to_dict()

[7]:

{'atoms': [(6, 0, 0, True, 0, 0, {}),
  (6, 0, 0, True, 0, 0, {}),
  (6, 0, 0, True, 0, 0, {}),
  (6, 0, 0, True, 0, 0, {}),
  (6, 0, 0, True, 0, 0, {}),
  (6, 0, 0, True, 0, 0, {}),
  (1, 0, 0, False, 0, 0, {}),
  (1, 0, 0, False, 0, 0, {}),
  (1, 0, 0, False, 0, 0, {}),
  (1, 0, 0, False, 0, 0, {}),
  (1, 0, 0, False, 0, 0, {}),
  (1, 0, 0, False, 0, 0, {})],
 'bonds': [(0, 1, 12, 0, {}),
  (0, 5, 12, 0, {}),
  (0, 6, 1, 0, {}),
  (1, 2, 12, 0, {}),
  (1, 7, 1, 0, {}),
  (2, 3, 12, 0, {}),
  (2, 8, 1, 0, {}),
  (3, 4, 12, 0, {}),
  (3, 9, 1, 0, {}),
  (4, 5, 12, 0, {}),
  (4, 10, 1, 0, {}),
  (5, 11, 1, 0, {})],
 'conformer': ("\x93NUMPY\x01\x00v\x00{'descr': '<f8', 'fortran_order': False, 'shape': (12, 3), }                                                         \nî|?5^ú9@\x02+\x87\x16ÙN\x15@\x04V\x0e-²\x1d\x13@\x85ëQ¸\x1ee:@²\x9dï§ÆK\x14@Ë¡E¶óý\x0b@×£p=\nW;@q=\n×£p\x17@\x9eï§ÆK7\x07@\x83ÀÊ¡EÖ;@Év¾\x9f\x1a¯\x1b@Zd;ßO\x8d\x0c@ìQ¸\x1e\x85k;@b\x10X9´È\x1c@\x06\x81\x95C\x8bl\x13@sh\x91í|\x7f:@j¼t\x93\x18\x84\x19@ÇK7\x89Aà\x15@í\x9e<,Ô:9@<NÑ\x91\\¾\x12@\x97ÿ\x90~ûú\x14@\x0f\x9c3¢´÷9@\x8d(í\r¾ð\x10@ð\x16HPü\x98\x07@ªñÒMb°;@¼\x05\x12\x14?\x86\x16@Ãdª`TRþ?¦\x9bÄ °\x92<@Ý$\x06\x81\x95C\x1e@Kê\x044\x11¶\x08@RI\x9d\x80&Ò;@\x02\x9a\x08\x1b\x9e\x1e @zÇ):\x92\x8b\x15@9EGrù/:@}?5^ºI\x1a@]mÅþ²û\x19@",
  {}),
 'molprops': {'ofe-name': 'benzene'},
 '__qualname__': 'SmallMoleculeComponent',
 '__module__': 'gufe.components.smallmoleculecomponent'}

As previously stated SmallMoleculeComponents also use the OpenFF backend to allow conversion between different object types. For example it’s possible to obtain an openff Molecule:

[8]:

type(ligand_mols[0].to_openff())

[8]:

openff.toolkit.topology.molecule.Molecule

Creating a network#

From these SmallMoleculeComponents we can quickly create a star map network which centers around the first ligand in our sdf file (benzene) using openfe.setup.ligand_network_planning.generate_radial_network.

Here we use Lomap (via the OpenFE interface LomapAtomMapper) to define the atom mappings between the various ligands and the central benzene structure. Whilst we use the defaults here, please note that the various supported arguments of Lomap can be passed to LomapAtomMapper.

Note: LomapAtomMapper is one of two currently implemented Mappers in OpenFE, the other being the rjmc mapper from Perses. In future work we will look to implement various other ones. Long term, users will be able to pass serveral mappers and atom mapping scoring methods on network generation.

[9]:

# Create network from the two molecules
from openfe.setup.ligand_network_planning import generate_radial_network
from openfe.setup import LomapAtomMapper

network = generate_radial_network(ligands=ligand_mols[1:],
                                  central_ligand=ligand_mols[0],
                                  mappers=[LomapAtomMapper(threed=True, element_change=False),])

[10]:

edges = [edge for edge in network.edges]
edge = edges[0]
edge
../_images/tutorials_showcase_notebook_20_0.png

This network contains a set of 6 edges centered around the benzene molecule which define the various atom mappings between the the transformation pairs.

Edges along the network can be accessed to recover the invidual molecules involved in that given alchemical tranformation, and the atom mapping between the two ligands.

Note: as can be seen in the example below, transformations are defined within OpenFE as going from componentA to componentB

[11]:

transform_edges = [edge for edge in network.edges]
print("molecule A smiles: ", transform_edges[0].componentA.smiles)
print("molecule B smiles: ", transform_edges[0].componentB.smiles)
print("map between molecule A and B: ", transform_edges[0].componentA_to_componentB)

molecule A smiles:  c1ccccc1
molecule B smiles:  O=Cc1ccccc1
map between molecule A and B:  {0: 3, 1: 4, 2: 5, 3: 6, 4: 7, 5: 8, 6: 9, 7: 10, 8: 11, 9: 12, 11: 13}

We can also visualise the atom mappings by invoking the individual OpenFE AtomMapping objects directly.

Here we show how to draw two mappings for benzene -> phenol and benzene -> anisole.

Unique atoms between each mapping are shown in red, and atoms which are mapped but undergo element changes are shown in blue. Bonds which either involve atoms that are unique or undergo element changes are highlighted in red.

[12]:

# Get the edge with phenol
edge = [edge for edge in network.edges if edge.componentB.name == "phenol"][0]
edge
../_images/tutorials_showcase_notebook_25_0.png 
[13]:

# Get edge for anisole
edge = [edge for edge in network.edges if edge.componentB.name == "anisole"][0]
edge
../_images/tutorials_showcase_notebook_26_0.png 
[14]:

from IPython.display import Image

# mappings can also be saved to file if required
edge = [edge for edge in network.edges if edge.componentB.name == "anisole"][0]
edge.draw_to_file('benzene-to-anisole.png')

# load it back for visualisation
Image("benzene-to-anisole.png")

[14]:
../_images/tutorials_showcase_notebook_27_0.png

JNK1 ligand network#

This is a rather simple atom mapping case. To show off the ability of the atom mapping, here is a network for the Schrodinger JNK1 dataset.

[15]:

# Load the jnk1 ligands
jnk1_sdf = Chem.SDMolSupplier('inputs/Jnk1_ligands.sdf', removeHs=False)

ligand_mols = [SmallMoleculeComponent(sdf) for sdf in jnk1_sdf]

# Create a network - reference molecule is ligand 0
jnk1_network = generate_radial_network(ligands=ligand_mols[1:],
                                       central_ligand=ligand_mols[0],
                                       mappers=[LomapAtomMapper(threed=True),])

[16]:

# Display all the atom mappings
jnk1_edges = [edge for edge in jnk1_network.edges]
for edge in jnk1_edges:
    display(edge)
../_images/tutorials_showcase_notebook_30_0.png
../_images/tutorials_showcase_notebook_30_1.png
../_images/tutorials_showcase_notebook_30_2.png
../_images/tutorials_showcase_notebook_30_3.png
../_images/tutorials_showcase_notebook_30_4.png
../_images/tutorials_showcase_notebook_30_5.png
../_images/tutorials_showcase_notebook_30_6.png
../_images/tutorials_showcase_notebook_30_7.png
../_images/tutorials_showcase_notebook_30_8.png
../_images/tutorials_showcase_notebook_30_9.png
../_images/tutorials_showcase_notebook_30_10.png
../_images/tutorials_showcase_notebook_30_11.png
../_images/tutorials_showcase_notebook_30_12.png
../_images/tutorials_showcase_notebook_30_13.png
../_images/tutorials_showcase_notebook_30_14.png
../_images/tutorials_showcase_notebook_30_15.png
../_images/tutorials_showcase_notebook_30_16.png
../_images/tutorials_showcase_notebook_30_17.png
../_images/tutorials_showcase_notebook_30_18.png
../_images/tutorials_showcase_notebook_30_19.png

Storing the network#

Created networks can easily be converted to (and also loaded from) as a GraphML representation.

This can allow users of OpenFE to store the network to disk for later use.

[17]:

# Convert to graphml
with open("network_store.graphml", "w") as writer:
    writer.write(network.to_graphml())

[18]:

from openfe.setup import LigandNetwork

# load a new network from this graphml representation
with open('network_store.graphml', 'r') as file:
    network_data = file.read()

new_network = LigandNetwork.from_graphml(network_data)

[19]:

edges = [edge for edge in new_network.edges]
print(f"edge 0 molecule 1: {edges[0].componentA.name}")
print(f"edge 0 molecule 2: {edges[0].componentB.name}")
print(f"edge 0 mapping: {edges[0].componentA_to_componentB}")

edge 0 molecule 1: benzene
edge 0 molecule 2: benzaldehyde
edge 0 mapping: {0: 3, 1: 4, 2: 5, 3: 6, 4: 7, 5: 8, 6: 9, 7: 10, 8: 11, 9: 12, 11: 13}

The OpenFE CLI#

The OpenFE toolkit also has a command line interface which we plan to add several convenience methods to.

For now functionality is limited to atom mapping, but it will be expanded upon as the project grows.

[20]:

# Call help on the OpenFE CLI
!openfe --help

Usage: openfe [OPTIONS] COMMAND [ARGS]...

  This is the command line tool to provide easy
  access to functionality from the OpenFE Python
  library.

Options:
  --version   Show the version and exit.
  --log PATH  logging configuration file
  -h, --help  Show this message and exit.

Network Planning Commands:
  plan-rbfe-network    Plan a relative binding
                       free energy network, saved
                       as JSON files for the
                       quickrun command.
  plan-rhfe-network    Plan a relative hydration
                       free energy network, saved
                       as JSON files for the
                       quickrun command.
  view-ligand-network  Visualize a ligand network

Quickrun Executor Commands:
  quickrun  Run a given transformation, saved as a
            JSON file
  gather    Gather result jsons for network of RFE
            results into a TSV file

Miscellaneous Commands:
  fetch  Fetch tutorial or other resource.
  test   Run the OpenFE test suite

[21]:

# Get an atom mapping using the CLI

!openfe atommapping --mapper LomapAtomMapper --mol inputs/benzene.sdf --mol inputs/styrene.sdf

{0: 5, 1: 6, 2: 7, 3: 8, 4: 9, 5: 10, 6: 11, 7: 12, 8: 13, 9: 14, 10: 4, 11: 15}

[22]:

# We can also directly visualise the mapping
!openfe atommapping --mapper LomapAtomMapper --mol inputs/benzene.sdf --mol inputs/styrene.sdf --output test.png

Image('test.png')

[22]:
../_images/tutorials_showcase_notebook_38_0.png

3. Running a Relative Ligand Binding Free Energy Calculation#

Now that we have a set of atom mappings defined, we know which atoms should undergo alchemical transformations to capture the free energy cost of transforming from one ligand to another.

To simulate this transformation we use the equilibrium RBFE protocol implemented in OpenFE. This uses OpenMM to run a Perses-like relative ligand binding free energy calculation using a single topology approach.

To achieve this simulation, the following steps need to happen:

  1. Create OpenMM systems of both end states

  2. Create a hybrid topology based on these defined endstates

  3. Set an appropriate Lambda schedule

  4. Set a MultiState reporter to write out appropriate coordinates and energies

  5. Create an OpenMM sampler (in this case we will be using a replica exchange sampler)

  6. Carry out the necessary simulation steps (minimization, equilibration, and production)

The RelativeHybridTopologyProtocol class in openfe.protocols.openmm_rfe implements a means to achieve all the above with minimal intervention.

Here we work through its usage for the benzene -> phenol binding free energy test case. As this involves both a relative binding free energy in solvent and complex phases, the RelativeHybridTopologyProtocol Protocol will be used to build two separate ProtocolDAG (directed-acyclic-graph) classes, one for each phase. These DAGs (which contain the necessary individual simulations), are then executed to yield the desired free energy results.

Note: the underlying components used for the creation of OpenMM hybrid topologies and samplers is still in flux, originating mostly from Perses. Please consider these to be in beta.

Defining the ChemicalSystems#

ChemicalSystems are OpenFE containers which define the various components which exist in a system of interest. You can consider these to be the nodes along an alchemical network which are connected by edges which carry out calculations along Alchemical states to get free energies.

ChemicalSystems take in three different things:

  1. A dictionary of the chemical components (e.g. SmallMoleculeComponent, ProteinComponent, SolventComponent) defining the system.

  2. Box vectors (optional), defining the shape and size of the unit cell of the system.

  3. An identifier name (optional), for the ChemicalSystem. This is used as part of the hash identifier of the ChemicalSystem, and can help distinguish between otherwise comparable systems.

In the case of a relative ligand binding free energy calculation for benzene -> phenol, four ChemicalSystems must be defined:

  1. Benzene in complex with T4 lysozyme in a box of water

  2. Phenol in complex with T4 lysozyme in a box of water

  3. Benzene in a box of water

  4. Phenol in a box of water

Here we will be passing the previously defined SmallMoleculeComponents for benzene and phenol. We will also pass a ProteinComponent generated from the PDB file present under inputs/181L_mod_capped_protonated.pdb. Finally, instead of passing in a specific box of water, we will define a SolventComponent which will contain the necessary information for OpenMM’s Modeller class to add water and 0.15 M NaCl around the solute when creating the OpenMM simulation objects.

[23]:

# First let's define the Protein and Solvent Components which we will be using
from openfe import SolventComponent, ProteinComponent
from openff.units import unit

protein = ProteinComponent.from_pdb_file('inputs/181L_mod_capped_protonated.pdb')

# Note: the distance from the solute to add water is not defined here but in the
# the relevant RBFE solver method
solvent = SolventComponent(positive_ion='Na', negative_ion='Cl',
                           neutralize=True, ion_concentration=0.15*unit.molar)

[24]:

# Extract the relevant edge for the benzene -> phenol transform in the radial graph
benz_to_phenol = [edge for edge in network.edges if edge.componentB.name == "phenol"][0]

benz_to_phenol
../_images/tutorials_showcase_notebook_44_0.png 
[25]:

# Let's create the four ChemicalSystems
from openfe import ChemicalSystem

benzene_complex = ChemicalSystem({'ligand': benz_to_phenol.componentA,
                                  'solvent': solvent,
                                  'protein': protein,})
benzene_solvent = ChemicalSystem({'ligand': benz_to_phenol.componentA,
                                  'solvent': solvent,})

phenol_complex = ChemicalSystem({'ligand': benz_to_phenol.componentB,
                                 'solvent': solvent,
                                 'protein': protein,})
phenol_solvent = ChemicalSystem({'ligand': benz_to_phenol.componentB,
                                 'solvent': solvent,})

Defining the RBFE simulation settings#

There are various different parameters which can be set to determine how the RBFE simulation will take place. To allow for maximum user flexibility, these are defined within openfe.setup.methods.openmm.equil_rbfe_methods as a series of settings objects which control the following:

  1. SystemSettings: parameters defining the simulation system, including; nonbonded_method, cutoff, constraints, water constraints, and hydrogen mass.

  2. TopologySettings: parameters defining the creation of the system topologies, including; force field, and solvent model.

  3. AlchemicalSettings: parameters controlling the creation of the hybrid topology system, and the lambda schedule. This includes various parameters ranging from softcore parameters, through to the number of lambda windows to sample.

  4. OpenMMEngineSettings: parameters determining how the OpenMM engine will execute the simulation. This mostly controls the compute platform which will be used to carry out the simulation.

  5. SamplerSettings: parameters determining which equilibrium sampler and their various controls parameters. For now only a replica exchange sampler is available, but one using self-adjusted mixture sampling will be added soon.

  6. BarostatSettings: parameters controling the creation of an OpenMM Monte Carlo barostat. Note: for now OpenFE only calculates RBFEs in NPT conditions. Support for NVT conditions may be added in the future.

  7. IntegratorSettings: parameters controlling the LangevinSplittingDynamicsMove integrator used for simulation.

  8. SimulationSettings: parameters controling the simulation plan, including the number of minimization steps, the length of the equilibration and production steps, the trajectory filename, write frequency, and which parts of the system to write coordinates for.

These various settings are combined together to create a RelativeLigandTransformSettings class. By default these settings use the values which are considered appropriate for RBFE calculations, however these are very system dependent and may not always be suitable for every case. A judicious choice of settings is always advised.

[26]:

# Settings can be accessed from the various classes

from openfe.protocols.openmm_rfe.equil_rfe_settings import (
    SystemSettings, SolvationSettings, AlchemicalSettings,
    OpenMMEngineSettings, AlchemicalSamplerSettings,
    IntegratorSettings, SimulationSettings
)

# The documentation on each class can be accessed to know
# what parameters can be set
?SystemSettings

[27]:

# Classes created without any arguments will use the default options
system = SystemSettings()
print(system)

nonbonded_method='PME' nonbonded_cutoff=<Quantity(1.0, 'nanometer')>

[28]:

# Or specific arguments can be passed to override the defaults
# Here we set the nonbonded_cutoff to 1.2 nm
system = SystemSettings(nonbonded_cutoff=1.2 * unit.nanometer)
print(system)

nonbonded_method='PME' nonbonded_cutoff=<Quantity(1.2, 'nanometer')>

The RelativeHybridTopologyProtocol class can directly populate the above set of default settings through its default_settings method.

[29]:

from openfe.protocols.openmm_rfe import RelativeHybridTopologyProtocol

rbfe_settings = RelativeHybridTopologyProtocol.default_settings()

[30]:

from pprint import pp

# Parameters can also be overriden after creation
# In this case, we'll reduce the equilibration length to 0.01 * nanosecond
# and the production to 0.05 * nanosecond in order to reduce the costs of
# running this notebook (in practice values of 2 and 5 nanoseconds
# respectively would be most appropriate)

rbfe_settings.simulation_settings.equilibration_length = 10 * unit.picosecond
rbfe_settings.simulation_settings.production_length = 50 * unit.picosecond

pp(rbfe_settings.simulation_settings)

SimulationSettings(equilibration_length=<Quantity(10, 'picosecond')>, production_length=<Quantity(50, 'picosecond')>, forcefield_cache='db.json', minimization_steps=5000, output_filename='simulation.nc', output_indices='not water', checkpoint_interval=<Quantity(250, 'timestep')>, checkpoint_storage='checkpoint.nc')

Creating the RelativeLigandTransform Protocol#

With the Settings inspected and adjusted, we can provide these to the Protocol. This Protocol defines the procedure to estimate a free energy difference between two chemical systems, with the details of the two end states yet to be defined.

[31]:

# Create RBFE Protocol class
rbfe_transform = RelativeHybridTopologyProtocol(
    settings=rbfe_settings
)

Creating the Protocol DAGs#

With the method we will be applying (the Protocol) defined, we can move onto applying to the alchemical transformation of interest.

The Protocol.create() method requires as input: - the two ChemicalSystem objects defining either end of the alchemical transformation - a mapping between the two systems, as a dict

This creates a directed-acyclic-graph (DAG) of computational tasks necessary for creating an estimate of the free energy difference between the two chemical systems.

As previously detailed, we create two sets of simulations, defining both the complex and solvent transformations.

[32]:

complex_dag = rbfe_transform.create(
    stateA=benzene_complex, stateB=phenol_complex,
    mapping={'ligand': benz_to_phenol},
)

solvent_dag = rbfe_transform.create(
    stateA=benzene_solvent, stateB=phenol_solvent,
    mapping={'ligand': benz_to_phenol},
)

The individual pieces of computational work are called Units. In this particular Protocol, the Units defined are three independent repeats of the alchemical transformation.

For other Protocols, for example non-equilibrium sampling routines, there might be dependencies between the tasks.

[33]:

list(complex_dag.protocol_units)

[33]:

[RelativeHybridTopologyProtocolUnit(benzene to phenol repeat 2 generation 0),
 RelativeHybridTopologyProtocolUnit(benzene to phenol repeat 1 generation 0),
 RelativeHybridTopologyProtocolUnit(benzene to phenol repeat 0 generation 0)]

Simulating the RelativeLigandTransforms#

Individual Units can then be executed by calling the .execute() method.

In the first instance we do a dry-run (which does everything but starting the simulation) to make sure that the hybrid openmm system can be constructed without any issues. Note: A successful call to .run() will return an empty Dictionary.

[34]:

# complex dry-run
complex_unit = list(complex_dag.protocol_units)[0]

complex_unit.run(dry=True, verbose=True)

INFO:   creating hybrid system
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   Generating a residue template for [H][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] using openff-2.0.0
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   Generating a residue template for [H][O][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] using openff-2.0.0
INFO:   creating hybrid system
INFO:   setting force field terms
INFO:   adding forces
INFO:   DONE
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases

Please cite the following:

        Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209
        Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27
        Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413
        Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w
        Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669


[34]:

{'debug': {'sampler': <instance of HybridRepexSampler>}}

[35]:

# solvent dry-run
solvent_unit = list(solvent_dag.protocol_units)[0]

solvent_unit.run(dry=True, verbose=True)

INFO:   creating hybrid system
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   creating hybrid system
INFO:   setting force field terms
INFO:   adding forces
INFO:   DONE
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases

Please cite the following:

        Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209
        Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27
        Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413
        Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w
        Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669


[35]:

{'debug': {'sampler': <instance of HybridRepexSampler>}}

Executing the simulations.#

The complex and solvent DAGs each contain many invdividual jobs. For convenience we can execute them sequentially in this notebook using the gufe.protocols.execute function.

In a more realistic (expansive) situation we would farm off the individual jobs to a HPC cluster or cloud compute service so they could be executed in parallel.

Note: we use the ``shared_basedir`` and ``scratch_basedir`` argument of ``execute_DAG`` in order to set the directory where the simulation files are written to

[36]:

from gufe.protocols import execute_DAG
import pathlib

[37]:

# Finally we can run the simulations
complex_path = pathlib.Path('./complex')
complex_path.mkdir()

# First the complex transformation
complex_dag_results = execute_DAG(complex_dag, scratch_basedir=complex_path, shared_basedir=complex_path)

INFO:   creating hybrid system
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   Generating a residue template for [H][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] using openff-2.0.0
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   Generating a residue template for [H][O][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] using openff-2.0.0
INFO:   creating hybrid system
INFO:   setting force field terms
INFO:   adding forces
INFO:   DONE
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases

Please cite the following:

        Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209
        Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27
        Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413
        Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w
        Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669


INFO:   minimizing systems
INFO:   equilibrating systems
INFO:   Equilibration iteration 1/10
INFO:   Iteration took 6.826s.
INFO:   Estimated completion (of equilibration only) in 0:01:01.478413, at Mon Jun 19 21:13:54 2023 (consuming total wall clock time 0:01:08.309348).
INFO:   Equilibration iteration 2/10
INFO:   Iteration took 4.048s.
INFO:   Estimated completion (of equilibration only) in 0:00:43.563226, at Mon Jun 19 21:13:40 2023 (consuming total wall clock time 0:00:54.454032).
INFO:   Equilibration iteration 3/10
INFO:   Iteration took 4.112s.
INFO:   Estimated completion (of equilibration only) in 0:00:35.025087, at Mon Jun 19 21:13:35 2023 (consuming total wall clock time 0:00:50.035838).
INFO:   Equilibration iteration 4/10
INFO:   Iteration took 4.084s.
INFO:   Estimated completion (of equilibration only) in 0:00:28.655503, at Mon Jun 19 21:13:33 2023 (consuming total wall clock time 0:00:47.759172).
INFO:   Equilibration iteration 5/10
INFO:   Iteration took 4.079s.
INFO:   Estimated completion (of equilibration only) in 0:00:23.190352, at Mon Jun 19 21:13:32 2023 (consuming total wall clock time 0:00:46.380704).
INFO:   Equilibration iteration 6/10
INFO:   Iteration took 4.084s.
INFO:   Estimated completion (of equilibration only) in 0:00:18.187013, at Mon Jun 19 21:13:31 2023 (consuming total wall clock time 0:00:45.467533).
INFO:   Equilibration iteration 7/10
INFO:   Iteration took 4.137s.
INFO:   Estimated completion (of equilibration only) in 0:00:13.466825, at Mon Jun 19 21:13:30 2023 (consuming total wall clock time 0:00:44.889416).
INFO:   Equilibration iteration 8/10
INFO:   Iteration took 4.190s.
INFO:   Estimated completion (of equilibration only) in 0:00:08.905241, at Mon Jun 19 21:13:30 2023 (consuming total wall clock time 0:00:44.526207).
INFO:   Equilibration iteration 9/10
INFO:   Iteration took 4.200s.
INFO:   Estimated completion (of equilibration only) in 0:00:04.425106, at Mon Jun 19 21:13:29 2023 (consuming total wall clock time 0:00:44.251061).
INFO:   Equilibration iteration 10/10
INFO:   Iteration took 4.144s.
INFO:   Estimated completion (of equilibration only) in 0:00:00, at Mon Jun 19 21:13:29 2023 (consuming total wall clock time 0:00:43.976222).
INFO:   running production phase
INFO:   ********************************************************************************
INFO:   Iteration 1/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.547s.
INFO:   Estimated completion in 0:03:43.214373, at 2023-Jun-19-21:17:17 (consuming total wall clock time 0:03:47.769768).
INFO:   ********************************************************************************
INFO:   Iteration 2/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.253s.
INFO:   Estimated completion in 0:03:31.763134, at 2023-Jun-19-21:17:10 (consuming total wall clock time 0:03:40.586598).
INFO:   ********************************************************************************
INFO:   Iteration 3/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.274s.
INFO:   Estimated completion in 0:03:25.423981, at 2023-Jun-19-21:17:08 (consuming total wall clock time 0:03:38.536150).
INFO:   ********************************************************************************
INFO:   Iteration 4/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.286s.
INFO:   Estimated completion in 0:03:20.201092, at 2023-Jun-19-21:17:07 (consuming total wall clock time 0:03:37.609882).
INFO:   ********************************************************************************
INFO:   Iteration 5/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.218s.
INFO:   Estimated completion in 0:03:14.723289, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.359210).
INFO:   ********************************************************************************
INFO:   Iteration 6/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.220s.
INFO:   Estimated completion in 0:03:09.705014, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.573879).
INFO:   ********************************************************************************
INFO:   Iteration 7/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.307s.
INFO:   Estimated completion in 0:03:05.416579, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.600673).
INFO:   ********************************************************************************
INFO:   Iteration 8/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.334s.
INFO:   Estimated completion in 0:03:01.273375, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.801637).
INFO:   ********************************************************************************
INFO:   Iteration 9/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.326s.
INFO:   Estimated completion in 0:02:57.054411, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.920014).
INFO:   ********************************************************************************
INFO:   Iteration 10/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.252s.
INFO:   Estimated completion in 0:02:52.539093, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.673866).
INFO:   ********************************************************************************
INFO:   Iteration 11/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.231s.
INFO:   Estimated completion in 0:02:47.976624, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.354646).
INFO:   ********************************************************************************
INFO:   Iteration 12/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.288s.
INFO:   Estimated completion in 0:02:43.659086, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.340902).
INFO:   ********************************************************************************
INFO:   Iteration 13/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.332s.
INFO:   Estimated completion in 0:02:39.451086, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.474441).
INFO:   ********************************************************************************
INFO:   Iteration 14/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.340s.
INFO:   Estimated completion in 0:02:35.253005, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.629174).
INFO:   ********************************************************************************
INFO:   Iteration 15/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.283s.
INFO:   Estimated completion in 0:02:30.902101, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.574430).
INFO:   ********************************************************************************
INFO:   Iteration 16/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.245s.
INFO:   Estimated completion in 0:02:26.481989, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.414690).
INFO:   ********************************************************************************
INFO:   Iteration 17/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.290s.
INFO:   Estimated completion in 0:02:22.172619, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.413059).
INFO:   ********************************************************************************
INFO:   Iteration 18/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.354s.
INFO:   Estimated completion in 0:02:17.964616, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.569712).
INFO:   ********************************************************************************
INFO:   Iteration 19/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.359s.
INFO:   Estimated completion in 0:02:13.760557, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.742835).
INFO:   ********************************************************************************
INFO:   Iteration 20/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.299s.
INFO:   Estimated completion in 0:02:09.436430, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.727384).
INFO:   ********************************************************************************
INFO:   Iteration 21/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.278s.
INFO:   Estimated completion in 0:02:05.089399, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.671378).
INFO:   ********************************************************************************
INFO:   Iteration 22/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.271s.
INFO:   Estimated completion in 0:02:00.743299, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.613034).
INFO:   ********************************************************************************
INFO:   Iteration 23/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.356s.
INFO:   Estimated completion in 0:01:56.494092, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.729800).
INFO:   ********************************************************************************
INFO:   Iteration 24/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.381s.
INFO:   Estimated completion in 0:01:52.262488, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.889399).
INFO:   ********************************************************************************
INFO:   Iteration 25/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.304s.
INFO:   Estimated completion in 0:01:47.941227, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.882454).
INFO:   ********************************************************************************
INFO:   Iteration 26/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.270s.
INFO:   Estimated completion in 0:01:43.591109, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.814810).
INFO:   ********************************************************************************
INFO:   Iteration 27/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.282s.
INFO:   Estimated completion in 0:01:39.257477, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.777123).
INFO:   ********************************************************************************
INFO:   Iteration 28/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.364s.
INFO:   Estimated completion in 0:01:34.986859, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.879224).
INFO:   ********************************************************************************
INFO:   Iteration 29/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.366s.
INFO:   Estimated completion in 0:01:30.716331, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.991263).
INFO:   ********************************************************************************
INFO:   Iteration 30/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.331s.
INFO:   Estimated completion in 0:01:26.413271, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:36.033177).
INFO:   ********************************************************************************
INFO:   Iteration 31/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.292s.
INFO:   Estimated completion in 0:01:22.081032, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:36.002715).
INFO:   ********************************************************************************
INFO:   Iteration 32/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.273s.
INFO:   Estimated completion in 0:01:17.739165, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:35.942126).
INFO:   ********************************************************************************
INFO:   Iteration 33/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.358s.
INFO:   Estimated completion in 0:01:13.444760, at 2023-Jun-19-21:17:05 (consuming total wall clock time 0:03:36.014001).
INFO:   ********************************************************************************
INFO:   Iteration 34/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.376s.
INFO:   Estimated completion in 0:01:09.158245, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.119515).
INFO:   ********************************************************************************
INFO:   Iteration 35/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.368s.
INFO:   Estimated completion in 0:01:04.862829, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.209430).
INFO:   ********************************************************************************
INFO:   Iteration 36/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.310s.
INFO:   Estimated completion in 0:01:00.537426, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.205091).
INFO:   ********************************************************************************
INFO:   Iteration 37/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.290s.
INFO:   Estimated completion in 0:00:56.205732, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.175894).
INFO:   ********************************************************************************
INFO:   Iteration 38/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.371s.
INFO:   Estimated completion in 0:00:51.899878, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.249492).
INFO:   ********************************************************************************
INFO:   Iteration 39/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.390s.
INFO:   Estimated completion in 0:00:47.597621, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.352821).
INFO:   ********************************************************************************
INFO:   Iteration 40/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.382s.
INFO:   Estimated completion in 0:00:43.287896, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.439482).
INFO:   ********************************************************************************
INFO:   Iteration 41/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.298s.
INFO:   Estimated completion in 0:00:38.955170, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.417609).
INFO:   ********************************************************************************
INFO:   Iteration 42/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.293s.
INFO:   Estimated completion in 0:00:34.622349, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.389679).
INFO:   ********************************************************************************
INFO:   Iteration 43/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.341s.
INFO:   Estimated completion in 0:00:30.299191, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.422796).
INFO:   ********************************************************************************
INFO:   Iteration 44/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.387s.
INFO:   Estimated completion in 0:00:25.980833, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.506942).
INFO:   ********************************************************************************
INFO:   Iteration 45/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.377s.
INFO:   Estimated completion in 0:00:21.657292, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.572921).
INFO:   ********************************************************************************
INFO:   Iteration 46/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.303s.
INFO:   Estimated completion in 0:00:17.324839, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.560482).
INFO:   ********************************************************************************
INFO:   Iteration 47/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.292s.
INFO:   Estimated completion in 0:00:12.991969, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.532823).
INFO:   ********************************************************************************
INFO:   Iteration 48/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.347s.
INFO:   Estimated completion in 0:00:08.662371, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.559275).
INFO:   ********************************************************************************
INFO:   Iteration 49/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.406s.
INFO:   Estimated completion in 0:00:04.333043, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.652126).
INFO:   ********************************************************************************
INFO:   Iteration 50/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.394s.
INFO:   Estimated completion in 0:00:00, at 2023-Jun-19-21:17:06 (consuming total wall clock time 0:03:36.725795).
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases
INFO:   creating hybrid system
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   Generating a residue template for [H][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] using openff-2.0.0
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   Generating a residue template for [H][O][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] using openff-2.0.0
INFO:   creating hybrid system
INFO:   setting force field terms
INFO:   adding forces
INFO:   DONE
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases

Please cite the following:

        Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209
        Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27
        Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413
        Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w
        Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669


INFO:   minimizing systems
INFO:   equilibrating systems
INFO:   Equilibration iteration 1/10
INFO:   Iteration took 5.225s.
INFO:   Estimated completion (of equilibration only) in 0:00:47.062479, at Mon Jun 19 21:20:18 2023 (consuming total wall clock time 0:00:52.291644).
INFO:   Equilibration iteration 2/10
INFO:   Iteration took 4.188s.
INFO:   Estimated completion (of equilibration only) in 0:00:37.698911, at Mon Jun 19 21:20:12 2023 (consuming total wall clock time 0:00:47.123638).
INFO:   Equilibration iteration 3/10
INFO:   Iteration took 4.204s.
INFO:   Estimated completion (of equilibration only) in 0:00:31.827871, at Mon Jun 19 21:20:11 2023 (consuming total wall clock time 0:00:45.468387).
INFO:   Equilibration iteration 4/10
INFO:   Iteration took 4.201s.
INFO:   Estimated completion (of equilibration only) in 0:00:26.776417, at Mon Jun 19 21:20:10 2023 (consuming total wall clock time 0:00:44.627361).
INFO:   Equilibration iteration 5/10
INFO:   Iteration took 4.159s.
INFO:   Estimated completion (of equilibration only) in 0:00:22.018026, at Mon Jun 19 21:20:09 2023 (consuming total wall clock time 0:00:44.036053).
INFO:   Equilibration iteration 6/10
INFO:   Iteration took 4.135s.
INFO:   Estimated completion (of equilibration only) in 0:00:17.441939, at Mon Jun 19 21:20:09 2023 (consuming total wall clock time 0:00:43.604847).
INFO:   Equilibration iteration 7/10
INFO:   Iteration took 4.187s.
INFO:   Estimated completion (of equilibration only) in 0:00:13.010224, at Mon Jun 19 21:20:09 2023 (consuming total wall clock time 0:00:43.367413).
INFO:   Equilibration iteration 8/10
INFO:   Iteration took 4.254s.
INFO:   Estimated completion (of equilibration only) in 0:00:08.656646, at Mon Jun 19 21:20:09 2023 (consuming total wall clock time 0:00:43.283229).
INFO:   Equilibration iteration 9/10
INFO:   Iteration took 4.225s.
INFO:   Estimated completion (of equilibration only) in 0:00:04.317968, at Mon Jun 19 21:20:08 2023 (consuming total wall clock time 0:00:43.179683).
INFO:   Equilibration iteration 10/10
INFO:   Iteration took 4.168s.
INFO:   Estimated completion (of equilibration only) in 0:00:00, at Mon Jun 19 21:20:08 2023 (consuming total wall clock time 0:00:43.035206).
INFO:   running production phase
INFO:   ********************************************************************************
INFO:   Iteration 1/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.521s.
INFO:   Estimated completion in 0:03:41.882403, at 2023-Jun-19-21:23:55 (consuming total wall clock time 0:03:46.410615).
INFO:   ********************************************************************************
INFO:   Iteration 2/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.251s.
INFO:   Estimated completion in 0:03:31.039049, at 2023-Jun-19-21:23:48 (consuming total wall clock time 0:03:39.832343).
INFO:   ********************************************************************************
INFO:   Iteration 3/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.286s.
INFO:   Estimated completion in 0:03:25.047605, at 2023-Jun-19-21:23:47 (consuming total wall clock time 0:03:38.135750).
INFO:   ********************************************************************************
INFO:   Iteration 4/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.310s.
INFO:   Estimated completion in 0:03:20.273311, at 2023-Jun-19-21:23:46 (consuming total wall clock time 0:03:37.688382).
INFO:   ********************************************************************************
INFO:   Iteration 5/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.231s.
INFO:   Estimated completion in 0:03:14.944897, at 2023-Jun-19-21:23:45 (consuming total wall clock time 0:03:36.605442).
INFO:   ********************************************************************************
INFO:   Iteration 6/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.210s.
INFO:   Estimated completion in 0:03:09.782337, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.661746).
INFO:   ********************************************************************************
INFO:   Iteration 7/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.258s.
INFO:   Estimated completion in 0:03:05.222426, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.374914).
INFO:   ********************************************************************************
INFO:   Iteration 8/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.333s.
INFO:   Estimated completion in 0:03:01.133230, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.634798).
INFO:   ********************************************************************************
INFO:   Iteration 9/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.333s.
INFO:   Estimated completion in 0:02:56.970268, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.817400).
INFO:   ********************************************************************************
INFO:   Iteration 10/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.302s.
INFO:   Estimated completion in 0:02:52.636252, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.795316).
INFO:   ********************************************************************************
INFO:   Iteration 11/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.229s.
INFO:   Estimated completion in 0:02:48.046179, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.443819).
INFO:   ********************************************************************************
INFO:   Iteration 12/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.264s.
INFO:   Estimated completion in 0:02:43.622064, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.292190).
INFO:   ********************************************************************************
INFO:   Iteration 13/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.326s.
INFO:   Estimated completion in 0:02:39.415709, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.426634).
INFO:   ********************************************************************************
INFO:   Iteration 14/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.352s.
INFO:   Estimated completion in 0:02:35.261218, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.640581).
INFO:   ********************************************************************************
INFO:   Iteration 15/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.288s.
INFO:   Estimated completion in 0:02:30.923376, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.604823).
INFO:   ********************************************************************************
INFO:   Iteration 16/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.244s.
INFO:   Estimated completion in 0:02:26.485332, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.419606).
INFO:   ********************************************************************************
INFO:   Iteration 17/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.256s.
INFO:   Estimated completion in 0:02:22.099680, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.302545).
INFO:   ********************************************************************************
INFO:   Iteration 18/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.332s.
INFO:   Estimated completion in 0:02:17.871927, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.424885).
INFO:   ********************************************************************************
INFO:   Iteration 19/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.389s.
INFO:   Estimated completion in 0:02:13.709207, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.660011).
INFO:   ********************************************************************************
INFO:   Iteration 20/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.294s.
INFO:   Estimated completion in 0:02:09.385334, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.642224).
INFO:   ********************************************************************************
INFO:   Iteration 21/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.238s.
INFO:   Estimated completion in 0:02:04.988956, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.498199).
INFO:   ********************************************************************************
INFO:   Iteration 22/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.249s.
INFO:   Estimated completion in 0:02:00.627171, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.405663).
INFO:   ********************************************************************************
INFO:   Iteration 23/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.327s.
INFO:   Estimated completion in 0:01:56.354656, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.471585).
INFO:   ********************************************************************************
INFO:   Iteration 24/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.352s.
INFO:   Estimated completion in 0:01:52.102295, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.581336).
INFO:   ********************************************************************************
INFO:   Iteration 25/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.354s.
INFO:   Estimated completion in 0:01:47.847647, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.695294).
INFO:   ********************************************************************************
INFO:   Iteration 26/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.256s.
INFO:   Estimated completion in 0:01:43.493435, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.611323).
INFO:   ********************************************************************************
INFO:   Iteration 27/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.274s.
INFO:   Estimated completion in 0:01:39.160089, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.565411).
INFO:   ********************************************************************************
INFO:   Iteration 28/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.343s.
INFO:   Estimated completion in 0:01:34.882813, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.642757).
INFO:   ********************************************************************************
INFO:   Iteration 29/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.347s.
INFO:   Estimated completion in 0:01:30.603191, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.721884).
INFO:   ********************************************************************************
INFO:   Iteration 30/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.365s.
INFO:   Estimated completion in 0:01:26.332463, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.831157).
INFO:   ********************************************************************************
INFO:   Iteration 31/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.287s.
INFO:   Estimated completion in 0:01:22.005429, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.803760).
INFO:   ********************************************************************************
INFO:   Iteration 32/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.274s.
INFO:   Estimated completion in 0:01:17.674145, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.761515).
INFO:   ********************************************************************************
INFO:   Iteration 33/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.349s.
INFO:   Estimated completion in 0:01:13.381503, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.827949).
INFO:   ********************************************************************************
INFO:   Iteration 34/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.360s.
INFO:   Estimated completion in 0:01:09.090451, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.907660).
INFO:   ********************************************************************************
INFO:   Iteration 35/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.363s.
INFO:   Estimated completion in 0:01:04.796431, at 2023-Jun-19-21:23:45 (consuming total wall clock time 0:03:35.988102).
INFO:   ********************************************************************************
INFO:   Iteration 36/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.308s.
INFO:   Estimated completion in 0:01:00.476074, at 2023-Jun-19-21:23:45 (consuming total wall clock time 0:03:35.985979).
INFO:   ********************************************************************************
INFO:   Iteration 37/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.276s.
INFO:   Estimated completion in 0:00:56.145111, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.942733).
INFO:   ********************************************************************************
INFO:   Iteration 38/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.329s.
INFO:   Estimated completion in 0:00:51.832244, at 2023-Jun-19-21:23:44 (consuming total wall clock time 0:03:35.967685).
INFO:   ********************************************************************************
INFO:   Iteration 39/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.381s.
INFO:   Estimated completion in 0:00:47.533535, at 2023-Jun-19-21:23:45 (consuming total wall clock time 0:03:36.061521).
INFO:   ********************************************************************************
INFO:   Iteration 40/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.383s.
INFO:   Estimated completion in 0:00:43.231821, at 2023-Jun-19-21:23:45 (consuming total wall clock time 0:03:36.159106).
INFO:   ********************************************************************************
INFO:   Iteration 41/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.326s.
INFO:   Estimated completion in 0:00:38.911438, at 2023-Jun-19-21:23:45 (consuming total wall clock time 0:03:36.174658).
INFO:   ********************************************************************************
INFO:   Iteration 42/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.300s.
INFO:   Estimated completion in 0:00:34.585345, at 2023-Jun-19-21:23:45 (consuming total wall clock time 0:03:36.158404).
INFO:   ********************************************************************************
INFO:   Iteration 43/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.350s.
INFO:   Estimated completion in 0:00:30.268124, at 2023-Jun-19-21:23:45 (consuming total wall clock time 0:03:36.200888).
INFO:   ********************************************************************************
INFO:   Iteration 44/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.384s.
INFO:   Estimated completion in 0:00:25.954521, at 2023-Jun-19-21:23:45 (consuming total wall clock time 0:03:36.287679).
INFO:   ********************************************************************************
INFO:   Iteration 45/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.394s.
INFO:   Estimated completion in 0:00:21.637650, at 2023-Jun-19-21:23:45 (consuming total wall clock time 0:03:36.376497).
INFO:   ********************************************************************************
INFO:   Iteration 46/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.338s.
INFO:   Estimated completion in 0:00:17.312523, at 2023-Jun-19-21:23:45 (consuming total wall clock time 0:03:36.406536).
INFO:   ********************************************************************************
INFO:   Iteration 47/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.296s.
INFO:   Estimated completion in 0:00:12.983311, at 2023-Jun-19-21:23:45 (consuming total wall clock time 0:03:36.388517).
INFO:   ********************************************************************************
INFO:   Iteration 48/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.413s.
INFO:   Estimated completion in 0:00:08.659783, at 2023-Jun-19-21:23:45 (consuming total wall clock time 0:03:36.494575).
INFO:   ********************************************************************************
INFO:   Iteration 49/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.391s.
INFO:   Estimated completion in 0:00:04.331318, at 2023-Jun-19-21:23:45 (consuming total wall clock time 0:03:36.565900).
INFO:   ********************************************************************************
INFO:   Iteration 50/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.402s.
INFO:   Estimated completion in 0:00:00, at 2023-Jun-19-21:23:45 (consuming total wall clock time 0:03:36.649609).
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases
INFO:   creating hybrid system
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   Generating a residue template for [H][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] using openff-2.0.0
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   Generating a residue template for [H][O][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] using openff-2.0.0
INFO:   creating hybrid system
INFO:   setting force field terms
INFO:   adding forces
INFO:   DONE
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases

Please cite the following:

        Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209
        Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27
        Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413
        Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w
        Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669


INFO:   minimizing systems
INFO:   equilibrating systems
INFO:   Equilibration iteration 1/10
INFO:   Iteration took 5.207s.
INFO:   Estimated completion (of equilibration only) in 0:00:46.900143, at Mon Jun 19 21:26:57 2023 (consuming total wall clock time 0:00:52.111270).
INFO:   Equilibration iteration 2/10
INFO:   Iteration took 4.155s.
INFO:   Estimated completion (of equilibration only) in 0:00:37.491912, at Mon Jun 19 21:26:52 2023 (consuming total wall clock time 0:00:46.864890).
INFO:   Equilibration iteration 3/10
INFO:   Iteration took 4.187s.
INFO:   Estimated completion (of equilibration only) in 0:00:31.652925, at Mon Jun 19 21:26:50 2023 (consuming total wall clock time 0:00:45.218464).
INFO:   Equilibration iteration 4/10
INFO:   Iteration took 4.184s.
INFO:   Estimated completion (of equilibration only) in 0:00:26.639013, at Mon Jun 19 21:26:50 2023 (consuming total wall clock time 0:00:44.398354).
INFO:   Equilibration iteration 5/10
INFO:   Iteration took 4.123s.
INFO:   Estimated completion (of equilibration only) in 0:00:21.893006, at Mon Jun 19 21:26:49 2023 (consuming total wall clock time 0:00:43.786012).
INFO:   Equilibration iteration 6/10
INFO:   Iteration took 4.137s.
INFO:   Estimated completion (of equilibration only) in 0:00:17.357732, at Mon Jun 19 21:26:49 2023 (consuming total wall clock time 0:00:43.394331).
INFO:   Equilibration iteration 7/10
INFO:   Iteration took 4.167s.
INFO:   Estimated completion (of equilibration only) in 0:00:12.949481, at Mon Jun 19 21:26:48 2023 (consuming total wall clock time 0:00:43.164937).
INFO:   Equilibration iteration 8/10
INFO:   Iteration took 4.220s.
INFO:   Estimated completion (of equilibration only) in 0:00:08.610423, at Mon Jun 19 21:26:48 2023 (consuming total wall clock time 0:00:43.052114).
INFO:   Equilibration iteration 9/10
INFO:   Iteration took 4.226s.
INFO:   Estimated completion (of equilibration only) in 0:00:04.296974, at Mon Jun 19 21:26:48 2023 (consuming total wall clock time 0:00:42.969742).
INFO:   Equilibration iteration 10/10
INFO:   Iteration took 4.183s.
INFO:   Estimated completion (of equilibration only) in 0:00:00, at Mon Jun 19 21:26:48 2023 (consuming total wall clock time 0:00:42.862653).
INFO:   running production phase
INFO:   ********************************************************************************
INFO:   Iteration 1/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.540s.
INFO:   Estimated completion in 0:03:42.796162, at 2023-Jun-19-21:30:36 (consuming total wall clock time 0:03:47.343023).
INFO:   ********************************************************************************
INFO:   Iteration 2/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.239s.
INFO:   Estimated completion in 0:03:31.172590, at 2023-Jun-19-21:30:28 (consuming total wall clock time 0:03:39.971448).
INFO:   ********************************************************************************
INFO:   Iteration 3/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.288s.
INFO:   Estimated completion in 0:03:25.270348, at 2023-Jun-19-21:30:27 (consuming total wall clock time 0:03:38.372711).
INFO:   ********************************************************************************
INFO:   Iteration 4/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.331s.
INFO:   Estimated completion in 0:03:20.677830, at 2023-Jun-19-21:30:26 (consuming total wall clock time 0:03:38.128076).
INFO:   ********************************************************************************
INFO:   Iteration 5/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.244s.
INFO:   Estimated completion in 0:03:15.351128, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:37.056808).
INFO:   ********************************************************************************
INFO:   Iteration 6/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.224s.
INFO:   Estimated completion in 0:03:10.240063, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.181890).
INFO:   ********************************************************************************
INFO:   Iteration 7/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.266s.
INFO:   Estimated completion in 0:03:05.660481, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:35.884280).
INFO:   ********************************************************************************
INFO:   Iteration 8/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.328s.
INFO:   Estimated completion in 0:03:01.487494, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:36.056541).
INFO:   ********************************************************************************
INFO:   Iteration 9/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.338s.
INFO:   Estimated completion in 0:02:57.315944, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.238956).
INFO:   ********************************************************************************
INFO:   Iteration 10/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.276s.
INFO:   Estimated completion in 0:02:52.854775, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:36.068469).
INFO:   ********************************************************************************
INFO:   Iteration 11/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.245s.
INFO:   Estimated completion in 0:02:48.328009, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:35.805139).
INFO:   ********************************************************************************
INFO:   Iteration 12/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.245s.
INFO:   Estimated completion in 0:02:43.816851, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:35.548488).
INFO:   ********************************************************************************
INFO:   Iteration 13/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.334s.
INFO:   Estimated completion in 0:02:39.603582, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:35.680516).
INFO:   ********************************************************************************
INFO:   Iteration 14/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.377s.
INFO:   Estimated completion in 0:02:35.493107, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:35.962649).
INFO:   ********************************************************************************
INFO:   Iteration 15/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.318s.
INFO:   Estimated completion in 0:02:31.194326, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:35.991894).
INFO:   ********************************************************************************
INFO:   Iteration 16/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.249s.
INFO:   Estimated completion in 0:02:26.753809, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:35.814424).
INFO:   ********************************************************************************
INFO:   Iteration 17/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.270s.
INFO:   Estimated completion in 0:02:22.369572, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:35.711473).
INFO:   ********************************************************************************
INFO:   Iteration 18/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.355s.
INFO:   Estimated completion in 0:02:18.142913, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:35.848302).
INFO:   ********************************************************************************
INFO:   Iteration 19/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.364s.
INFO:   Estimated completion in 0:02:13.927217, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:36.011641).
INFO:   ********************************************************************************
INFO:   Iteration 20/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.357s.
INFO:   Estimated completion in 0:02:09.678932, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:36.131554).
INFO:   ********************************************************************************
INFO:   Iteration 21/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.274s.
INFO:   Estimated completion in 0:02:05.307815, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:36.047957).
INFO:   ********************************************************************************
INFO:   Iteration 22/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.271s.
INFO:   Estimated completion in 0:02:00.942370, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:35.968517).
INFO:   ********************************************************************************
INFO:   Iteration 23/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.347s.
INFO:   Estimated completion in 0:01:56.671617, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:36.058550).
INFO:   ********************************************************************************
INFO:   Iteration 24/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.362s.
INFO:   Estimated completion in 0:01:52.406777, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:36.166878).
INFO:   ********************************************************************************
INFO:   Iteration 25/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.360s.
INFO:   Estimated completion in 0:01:48.134471, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.268941).
INFO:   ********************************************************************************
INFO:   Iteration 26/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.266s.
INFO:   Estimated completion in 0:01:43.765696, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.178533).
INFO:   ********************************************************************************
INFO:   Iteration 27/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.279s.
INFO:   Estimated completion in 0:01:39.415022, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:36.119613).
INFO:   ********************************************************************************
INFO:   Iteration 28/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.318s.
INFO:   Estimated completion in 0:01:35.097483, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:36.130643).
INFO:   ********************************************************************************
INFO:   Iteration 29/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.340s.
INFO:   Estimated completion in 0:01:30.799067, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.188255).
INFO:   ********************************************************************************
INFO:   Iteration 30/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.366s.
INFO:   Estimated completion in 0:01:26.511497, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.278743).
INFO:   ********************************************************************************
INFO:   Iteration 31/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.284s.
INFO:   Estimated completion in 0:01:22.165926, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.226121).
INFO:   ********************************************************************************
INFO:   Iteration 32/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.271s.
INFO:   Estimated completion in 0:01:17.819107, at 2023-Jun-19-21:30:24 (consuming total wall clock time 0:03:36.164185).
INFO:   ********************************************************************************
INFO:   Iteration 33/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.343s.
INFO:   Estimated completion in 0:01:13.511242, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.209534).
INFO:   ********************************************************************************
INFO:   Iteration 34/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.390s.
INFO:   Estimated completion in 0:01:09.224974, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.328043).
INFO:   ********************************************************************************
INFO:   Iteration 35/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.386s.
INFO:   Estimated completion in 0:01:04.928237, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.427456).
INFO:   ********************************************************************************
INFO:   Iteration 36/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.331s.
INFO:   Estimated completion in 0:01:00.606105, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.450374).
INFO:   ********************************************************************************
INFO:   Iteration 37/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.287s.
INFO:   Estimated completion in 0:00:56.265965, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.407557).
INFO:   ********************************************************************************
INFO:   Iteration 38/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.342s.
INFO:   Estimated completion in 0:00:51.946093, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.442053).
INFO:   ********************************************************************************
INFO:   Iteration 39/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.382s.
INFO:   Estimated completion in 0:00:47.635475, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.524888).
INFO:   ********************************************************************************
INFO:   Iteration 40/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.375s.
INFO:   Estimated completion in 0:00:43.319420, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.597102).
INFO:   ********************************************************************************
INFO:   Iteration 41/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.333s.
INFO:   Estimated completion in 0:00:38.990649, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.614717).
INFO:   ********************************************************************************
INFO:   Iteration 42/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.301s.
INFO:   Estimated completion in 0:00:34.653873, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.586704).
INFO:   ********************************************************************************
INFO:   Iteration 43/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.340s.
INFO:   Estimated completion in 0:00:30.325738, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.612417).
INFO:   ********************************************************************************
INFO:   Iteration 44/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.405s.
INFO:   Estimated completion in 0:00:26.005191, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.709925).
INFO:   ********************************************************************************
INFO:   Iteration 45/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.391s.
INFO:   Estimated completion in 0:00:21.678473, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.784734).
INFO:   ********************************************************************************
INFO:   Iteration 46/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.376s.
INFO:   Estimated completion in 0:00:17.347449, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.843113).
INFO:   ********************************************************************************
INFO:   Iteration 47/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.320s.
INFO:   Estimated completion in 0:00:13.010397, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.839952).
INFO:   ********************************************************************************
INFO:   Iteration 48/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.352s.
INFO:   Estimated completion in 0:00:08.674748, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.868691).
INFO:   ********************************************************************************
INFO:   Iteration 49/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.409s.
INFO:   Estimated completion in 0:00:04.339159, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:36.957964).
INFO:   ********************************************************************************
INFO:   Iteration 50/50
INFO:   ********************************************************************************
INFO:   Iteration took 4.415s.
INFO:   Estimated completion in 0:00:00, at 2023-Jun-19-21:30:25 (consuming total wall clock time 0:03:37.051086).
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases

[38]:

# Next the solvent state transformation
solvent_path = pathlib.Path('./solvent')
solvent_path.mkdir()

solvent_dag_results = execute_DAG(solvent_dag, scratch_basedir=solvent_path, shared_basedir=solvent_path)

INFO:   creating hybrid system
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   Generating a residue template for [H][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] using openff-2.0.0
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   Generating a residue template for [H][O][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] using openff-2.0.0
INFO:   creating hybrid system
INFO:   setting force field terms
INFO:   adding forces
INFO:   DONE
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases
INFO:   minimizing systems

Please cite the following:

        Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209
        Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27
        Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413
        Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w
        Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669


INFO:   equilibrating systems
INFO:   Equilibration iteration 1/10
INFO:   Iteration took 1.585s.
INFO:   Estimated completion (of equilibration only) in 0:00:14.289953, at Mon Jun 19 21:31:05 2023 (consuming total wall clock time 0:00:15.877726).
INFO:   Equilibration iteration 2/10
INFO:   Iteration took 0.620s.
INFO:   Estimated completion (of equilibration only) in 0:00:08.854433, at Mon Jun 19 21:31:01 2023 (consuming total wall clock time 0:00:11.068041).
INFO:   Equilibration iteration 3/10
INFO:   Iteration took 0.619s.
INFO:   Estimated completion (of equilibration only) in 0:00:06.622818, at Mon Jun 19 21:30:59 2023 (consuming total wall clock time 0:00:09.461168).
INFO:   Equilibration iteration 4/10
INFO:   Iteration took 0.620s.
INFO:   Estimated completion (of equilibration only) in 0:00:05.195098, at Mon Jun 19 21:30:58 2023 (consuming total wall clock time 0:00:08.658497).
INFO:   Equilibration iteration 5/10
INFO:   Iteration took 0.623s.
INFO:   Estimated completion (of equilibration only) in 0:00:04.094208, at Mon Jun 19 21:30:58 2023 (consuming total wall clock time 0:00:08.188416).
INFO:   Equilibration iteration 6/10
INFO:   Iteration took 0.623s.
INFO:   Estimated completion (of equilibration only) in 0:00:03.147873, at Mon Jun 19 21:30:57 2023 (consuming total wall clock time 0:00:07.869683).
INFO:   Equilibration iteration 7/10
INFO:   Iteration took 0.620s.
INFO:   Estimated completion (of equilibration only) in 0:00:02.292606, at Mon Jun 19 21:30:57 2023 (consuming total wall clock time 0:00:07.642020).
INFO:   Equilibration iteration 8/10
INFO:   Iteration took 0.620s.
INFO:   Estimated completion (of equilibration only) in 0:00:01.493686, at Mon Jun 19 21:30:57 2023 (consuming total wall clock time 0:00:07.468429).
INFO:   Equilibration iteration 9/10
INFO:   Iteration took 0.623s.
INFO:   Estimated completion (of equilibration only) in 0:00:00.733940, at Mon Jun 19 21:30:57 2023 (consuming total wall clock time 0:00:07.339395).
INFO:   Equilibration iteration 10/10
INFO:   Iteration took 0.623s.
INFO:   Estimated completion (of equilibration only) in 0:00:00, at Mon Jun 19 21:30:57 2023 (consuming total wall clock time 0:00:07.234573).
INFO:   running production phase
INFO:   ********************************************************************************
INFO:   Iteration 1/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.648s.
INFO:   Estimated completion in 0:00:32.170292, at 2023-Jun-19-21:31:30 (consuming total wall clock time 0:00:32.826829).
INFO:   ********************************************************************************
INFO:   Iteration 2/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.637s.
INFO:   Estimated completion in 0:00:31.292839, at 2023-Jun-19-21:31:29 (consuming total wall clock time 0:00:32.596707).
INFO:   ********************************************************************************
INFO:   Iteration 3/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.640s.
INFO:   Estimated completion in 0:00:30.610896, at 2023-Jun-19-21:31:29 (consuming total wall clock time 0:00:32.564783).
INFO:   ********************************************************************************
INFO:   Iteration 4/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.640s.
INFO:   Estimated completion in 0:00:29.962932, at 2023-Jun-19-21:31:29 (consuming total wall clock time 0:00:32.568404).
INFO:   ********************************************************************************
INFO:   Iteration 5/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.635s.
INFO:   Estimated completion in 0:00:29.259954, at 2023-Jun-19-21:31:29 (consuming total wall clock time 0:00:32.511060).
INFO:   ********************************************************************************
INFO:   Iteration 6/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.635s.
INFO:   Estimated completion in 0:00:28.598301, at 2023-Jun-19-21:31:29 (consuming total wall clock time 0:00:32.498070).
INFO:   ********************************************************************************
INFO:   Iteration 7/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.680s.
INFO:   Estimated completion in 0:00:28.190088, at 2023-Jun-19-21:31:30 (consuming total wall clock time 0:00:32.779172).
INFO:   ********************************************************************************
INFO:   Iteration 8/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.676s.
INFO:   Estimated completion in 0:00:27.723383, at 2023-Jun-19-21:31:30 (consuming total wall clock time 0:00:33.004028).
INFO:   ********************************************************************************
INFO:   Iteration 9/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.681s.
INFO:   Estimated completion in 0:00:27.240135, at 2023-Jun-19-21:31:30 (consuming total wall clock time 0:00:33.219677).
INFO:   ********************************************************************************
INFO:   Iteration 10/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.688s.
INFO:   Estimated completion in 0:00:26.732145, at 2023-Jun-19-21:31:30 (consuming total wall clock time 0:00:33.415182).
INFO:   ********************************************************************************
INFO:   Iteration 11/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.707s.
INFO:   Estimated completion in 0:00:26.262401, at 2023-Jun-19-21:31:30 (consuming total wall clock time 0:00:33.669745).
INFO:   ********************************************************************************
INFO:   Iteration 12/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.697s.
INFO:   Estimated completion in 0:00:25.712197, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.831838).
INFO:   ********************************************************************************
INFO:   Iteration 13/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.704s.
INFO:   Estimated completion in 0:00:25.151505, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.988520).
INFO:   ********************************************************************************
INFO:   Iteration 14/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.695s.
INFO:   Estimated completion in 0:00:24.533536, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.074356).
INFO:   ********************************************************************************
INFO:   Iteration 15/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.694s.
INFO:   Estimated completion in 0:00:23.902212, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.146016).
INFO:   ********************************************************************************
INFO:   Iteration 16/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.691s.
INFO:   Estimated completion in 0:00:23.258744, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.204035).
INFO:   ********************************************************************************
INFO:   Iteration 17/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.695s.
INFO:   Estimated completion in 0:00:22.615520, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.265940).
INFO:   ********************************************************************************
INFO:   Iteration 18/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.696s.
INFO:   Estimated completion in 0:00:21.968090, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.325141).
INFO:   ********************************************************************************
INFO:   Iteration 19/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.692s.
INFO:   Estimated completion in 0:00:21.307938, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.367642).
INFO:   ********************************************************************************
INFO:   Iteration 20/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.688s.
INFO:   Estimated completion in 0:00:20.643481, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.405801).
INFO:   ********************************************************************************
INFO:   Iteration 21/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.694s.
INFO:   Estimated completion in 0:00:19.987437, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.461099).
INFO:   ********************************************************************************
INFO:   Iteration 22/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.700s.
INFO:   Estimated completion in 0:00:19.331315, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.520205).
INFO:   ********************************************************************************
INFO:   Iteration 23/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.693s.
INFO:   Estimated completion in 0:00:18.661462, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.558263).
INFO:   ********************************************************************************
INFO:   Iteration 24/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.652s.
INFO:   Estimated completion in 0:00:17.947680, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.514769).
INFO:   ********************************************************************************
INFO:   Iteration 25/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.641s.
INFO:   Estimated completion in 0:00:17.217753, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.435506).
INFO:   ********************************************************************************
INFO:   Iteration 26/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.638s.
INFO:   Estimated completion in 0:00:16.493047, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.360514).
INFO:   ********************************************************************************
INFO:   Iteration 27/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.634s.
INFO:   Estimated completion in 0:00:15.773467, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.290145).
INFO:   ********************************************************************************
INFO:   Iteration 28/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.639s.
INFO:   Estimated completion in 0:00:15.063624, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.235508).
INFO:   ********************************************************************************
INFO:   Iteration 29/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.639s.
INFO:   Estimated completion in 0:00:14.351371, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.169930).
INFO:   ********************************************************************************
INFO:   Iteration 30/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.637s.
INFO:   Estimated completion in 0:00:13.647003, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.117508).
INFO:   ********************************************************************************
INFO:   Iteration 31/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.640s.
INFO:   Estimated completion in 0:00:12.947422, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.072163).
INFO:   ********************************************************************************
INFO:   Iteration 32/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.637s.
INFO:   Estimated completion in 0:00:12.248601, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.023891).
INFO:   ********************************************************************************
INFO:   Iteration 33/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.635s.
INFO:   Estimated completion in 0:00:11.553360, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.980471).
INFO:   ********************************************************************************
INFO:   Iteration 34/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.631s.
INFO:   Estimated completion in 0:00:10.857251, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.928909).
INFO:   ********************************************************************************
INFO:   Iteration 35/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.636s.
INFO:   Estimated completion in 0:00:10.164662, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.882205).
INFO:   ********************************************************************************
INFO:   Iteration 36/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.635s.
INFO:   Estimated completion in 0:00:09.476971, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.846324).
INFO:   ********************************************************************************
INFO:   Iteration 37/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.632s.
INFO:   Estimated completion in 0:00:08.787516, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.798140).
INFO:   ********************************************************************************
INFO:   Iteration 38/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.632s.
INFO:   Estimated completion in 0:00:08.101584, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.756601).
INFO:   ********************************************************************************
INFO:   Iteration 39/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.661s.
INFO:   Estimated completion in 0:00:07.426448, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.756581).
INFO:   ********************************************************************************
INFO:   Iteration 40/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.665s.
INFO:   Estimated completion in 0:00:06.751504, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.757521).
INFO:   ********************************************************************************
INFO:   Iteration 41/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.692s.
INFO:   Estimated completion in 0:00:06.083136, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.795203).
INFO:   ********************************************************************************
INFO:   Iteration 42/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.693s.
INFO:   Estimated completion in 0:00:05.413352, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.833449).
INFO:   ********************************************************************************
INFO:   Iteration 43/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.686s.
INFO:   Estimated completion in 0:00:04.740519, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.860852).
INFO:   ********************************************************************************
INFO:   Iteration 44/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.688s.
INFO:   Estimated completion in 0:00:04.067517, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.895974).
INFO:   ********************************************************************************
INFO:   Iteration 45/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.699s.
INFO:   Estimated completion in 0:00:03.393776, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.937759).
INFO:   ********************************************************************************
INFO:   Iteration 46/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.685s.
INFO:   Estimated completion in 0:00:02.716450, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.955625).
INFO:   ********************************************************************************
INFO:   Iteration 47/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.685s.
INFO:   Estimated completion in 0:00:02.038385, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.973082).
INFO:   ********************************************************************************
INFO:   Iteration 48/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.691s.
INFO:   Estimated completion in 0:00:01.359940, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:33.998497).
INFO:   ********************************************************************************
INFO:   Iteration 49/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.701s.
INFO:   Estimated completion in 0:00:00.680658, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.032893).
INFO:   ********************************************************************************
INFO:   Iteration 50/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.692s.
INFO:   Estimated completion in 0:00:00, at 2023-Jun-19-21:31:31 (consuming total wall clock time 0:00:34.057417).
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases
INFO:   creating hybrid system
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   Generating a residue template for [H][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] using openff-2.0.0
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   Generating a residue template for [H][O][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] using openff-2.0.0
INFO:   creating hybrid system
INFO:   setting force field terms
INFO:   adding forces
INFO:   DONE
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases
INFO:   minimizing systems

Please cite the following:

        Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209
        Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27
        Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413
        Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w
        Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669


INFO:   equilibrating systems
INFO:   Equilibration iteration 1/10
INFO:   Iteration took 0.978s.
INFO:   Estimated completion (of equilibration only) in 0:00:08.815932, at Mon Jun 19 21:31:58 2023 (consuming total wall clock time 0:00:09.795480).
INFO:   Equilibration iteration 2/10
INFO:   Iteration took 0.672s.
INFO:   Estimated completion (of equilibration only) in 0:00:06.630092, at Mon Jun 19 21:31:56 2023 (consuming total wall clock time 0:00:08.287615).
INFO:   Equilibration iteration 3/10
INFO:   Iteration took 0.662s.
INFO:   Estimated completion (of equilibration only) in 0:00:05.427368, at Mon Jun 19 21:31:56 2023 (consuming total wall clock time 0:00:07.753383).
INFO:   Equilibration iteration 4/10
INFO:   Iteration took 0.673s.
INFO:   Estimated completion (of equilibration only) in 0:00:04.510628, at Mon Jun 19 21:31:56 2023 (consuming total wall clock time 0:00:07.517713).
INFO:   Equilibration iteration 5/10
INFO:   Iteration took 0.679s.
INFO:   Estimated completion (of equilibration only) in 0:00:03.693438, at Mon Jun 19 21:31:56 2023 (consuming total wall clock time 0:00:07.386876).
INFO:   Equilibration iteration 6/10
INFO:   Iteration took 0.668s.
INFO:   Estimated completion (of equilibration only) in 0:00:02.914076, at Mon Jun 19 21:31:55 2023 (consuming total wall clock time 0:00:07.285191).
INFO:   Equilibration iteration 7/10
INFO:   Iteration took 0.666s.
INFO:   Estimated completion (of equilibration only) in 0:00:02.161904, at Mon Jun 19 21:31:55 2023 (consuming total wall clock time 0:00:07.206348).
INFO:   Equilibration iteration 8/10
INFO:   Iteration took 0.663s.
INFO:   Estimated completion (of equilibration only) in 0:00:01.428631, at Mon Jun 19 21:31:55 2023 (consuming total wall clock time 0:00:07.143156).
INFO:   Equilibration iteration 9/10
INFO:   Iteration took 0.669s.
INFO:   Estimated completion (of equilibration only) in 0:00:00.710090, at Mon Jun 19 21:31:55 2023 (consuming total wall clock time 0:00:07.100899).
INFO:   Equilibration iteration 10/10
INFO:   Iteration took 0.671s.
INFO:   Estimated completion (of equilibration only) in 0:00:00, at Mon Jun 19 21:31:55 2023 (consuming total wall clock time 0:00:07.070671).
INFO:   running production phase
INFO:   ********************************************************************************
INFO:   Iteration 1/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.710s.
INFO:   Estimated completion in 0:00:35.168714, at 2023-Jun-19-21:32:31 (consuming total wall clock time 0:00:35.886443).
INFO:   ********************************************************************************
INFO:   Iteration 2/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.690s.
INFO:   Estimated completion in 0:00:34.011452, at 2023-Jun-19-21:32:31 (consuming total wall clock time 0:00:35.428596).
INFO:   ********************************************************************************
INFO:   Iteration 3/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.663s.
INFO:   Estimated completion in 0:00:32.731562, at 2023-Jun-19-21:32:30 (consuming total wall clock time 0:00:34.820811).
INFO:   ********************************************************************************
INFO:   Iteration 4/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.645s.
INFO:   Estimated completion in 0:00:31.605314, at 2023-Jun-19-21:32:30 (consuming total wall clock time 0:00:34.353602).
INFO:   ********************************************************************************
INFO:   Iteration 5/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.634s.
INFO:   Estimated completion in 0:00:30.568407, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.964896).
INFO:   ********************************************************************************
INFO:   Iteration 6/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.638s.
INFO:   Estimated completion in 0:00:29.647156, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.689950).
INFO:   ********************************************************************************
INFO:   Iteration 7/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.645s.
INFO:   Estimated completion in 0:00:28.847111, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.543152).
INFO:   ********************************************************************************
INFO:   Iteration 8/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.629s.
INFO:   Estimated completion in 0:00:28.020181, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.357358).
INFO:   ********************************************************************************
INFO:   Iteration 9/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.632s.
INFO:   Estimated completion in 0:00:27.255959, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.238974).
INFO:   ********************************************************************************
INFO:   Iteration 10/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.628s.
INFO:   Estimated completion in 0:00:26.500947, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.126184).
INFO:   ********************************************************************************
INFO:   Iteration 11/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.630s.
INFO:   Estimated completion in 0:00:25.762794, at 2023-Jun-19-21:32:28 (consuming total wall clock time 0:00:33.029224).
INFO:   ********************************************************************************
INFO:   Iteration 12/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.632s.
INFO:   Estimated completion in 0:00:25.040895, at 2023-Jun-19-21:32:28 (consuming total wall clock time 0:00:32.948546).
INFO:   ********************************************************************************
INFO:   Iteration 13/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.634s.
INFO:   Estimated completion in 0:00:24.340988, at 2023-Jun-19-21:32:28 (consuming total wall clock time 0:00:32.893227).
INFO:   ********************************************************************************
INFO:   Iteration 14/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.630s.
INFO:   Estimated completion in 0:00:23.648233, at 2023-Jun-19-21:32:28 (consuming total wall clock time 0:00:32.844768).
INFO:   ********************************************************************************
INFO:   Iteration 15/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.630s.
INFO:   Estimated completion in 0:00:22.962388, at 2023-Jun-19-21:32:28 (consuming total wall clock time 0:00:32.803411).
INFO:   ********************************************************************************
INFO:   Iteration 16/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.629s.
INFO:   Estimated completion in 0:00:22.281917, at 2023-Jun-19-21:32:28 (consuming total wall clock time 0:00:32.767525).
INFO:   ********************************************************************************
INFO:   Iteration 17/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.636s.
INFO:   Estimated completion in 0:00:21.614499, at 2023-Jun-19-21:32:28 (consuming total wall clock time 0:00:32.749241).
INFO:   ********************************************************************************
INFO:   Iteration 18/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.633s.
INFO:   Estimated completion in 0:00:20.938675, at 2023-Jun-19-21:32:28 (consuming total wall clock time 0:00:32.716679).
INFO:   ********************************************************************************
INFO:   Iteration 19/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.670s.
INFO:   Estimated completion in 0:00:20.334488, at 2023-Jun-19-21:32:28 (consuming total wall clock time 0:00:32.797562).
INFO:   ********************************************************************************
INFO:   Iteration 20/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.684s.
INFO:   Estimated completion in 0:00:19.735747, at 2023-Jun-19-21:32:28 (consuming total wall clock time 0:00:32.892912).
INFO:   ********************************************************************************
INFO:   Iteration 21/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.672s.
INFO:   Estimated completion in 0:00:19.111996, at 2023-Jun-19-21:32:28 (consuming total wall clock time 0:00:32.951717).
INFO:   ********************************************************************************
INFO:   Iteration 22/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.696s.
INFO:   Estimated completion in 0:00:18.517882, at 2023-Jun-19-21:32:28 (consuming total wall clock time 0:00:33.067647).
INFO:   ********************************************************************************
INFO:   Iteration 23/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.697s.
INFO:   Estimated completion in 0:00:17.912640, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.171556).
INFO:   ********************************************************************************
INFO:   Iteration 24/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.695s.
INFO:   Estimated completion in 0:00:17.294235, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.258144).
INFO:   ********************************************************************************
INFO:   Iteration 25/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.685s.
INFO:   Estimated completion in 0:00:16.658333, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.316667).
INFO:   ********************************************************************************
INFO:   Iteration 26/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.686s.
INFO:   Estimated completion in 0:00:16.025147, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.385722).
INFO:   ********************************************************************************
INFO:   Iteration 27/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.682s.
INFO:   Estimated completion in 0:00:15.383898, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.443257).
INFO:   ********************************************************************************
INFO:   Iteration 28/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.691s.
INFO:   Estimated completion in 0:00:14.742576, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.505854).
INFO:   ********************************************************************************
INFO:   Iteration 29/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.687s.
INFO:   Estimated completion in 0:00:14.091660, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.551572).
INFO:   ********************************************************************************
INFO:   Iteration 30/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.685s.
INFO:   Estimated completion in 0:00:13.436244, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.590611).
INFO:   ********************************************************************************
INFO:   Iteration 31/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.699s.
INFO:   Estimated completion in 0:00:12.787881, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.652319).
INFO:   ********************************************************************************
INFO:   Iteration 32/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.681s.
INFO:   Estimated completion in 0:00:12.126836, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.685654).
INFO:   ********************************************************************************
INFO:   Iteration 33/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.685s.
INFO:   Estimated completion in 0:00:11.464046, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.717784).
INFO:   ********************************************************************************
INFO:   Iteration 34/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.680s.
INFO:   Estimated completion in 0:00:10.797898, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.743433).
INFO:   ********************************************************************************
INFO:   Iteration 35/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.685s.
INFO:   Estimated completion in 0:00:10.131987, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.773291).
INFO:   ********************************************************************************
INFO:   Iteration 36/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.684s.
INFO:   Estimated completion in 0:00:09.464515, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.801838).
INFO:   ********************************************************************************
INFO:   Iteration 37/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.634s.
INFO:   Estimated completion in 0:00:08.778810, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.764655).
INFO:   ********************************************************************************
INFO:   Iteration 38/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.641s.
INFO:   Estimated completion in 0:00:08.095912, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.732966).
INFO:   ********************************************************************************
INFO:   Iteration 39/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.633s.
INFO:   Estimated completion in 0:00:07.412655, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.693886).
INFO:   ********************************************************************************
INFO:   Iteration 40/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.630s.
INFO:   Estimated completion in 0:00:06.730475, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.652375).
INFO:   ********************************************************************************
INFO:   Iteration 41/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.632s.
INFO:   Estimated completion in 0:00:06.050597, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.614426).
INFO:   ********************************************************************************
INFO:   Iteration 42/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.634s.
INFO:   Estimated completion in 0:00:05.372764, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.579778).
INFO:   ********************************************************************************
INFO:   Iteration 43/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.632s.
INFO:   Estimated completion in 0:00:04.696191, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.544222).
INFO:   ********************************************************************************
INFO:   Iteration 44/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.634s.
INFO:   Estimated completion in 0:00:04.022158, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.517981).
INFO:   ********************************************************************************
INFO:   Iteration 45/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.629s.
INFO:   Estimated completion in 0:00:03.348218, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.482183).
INFO:   ********************************************************************************
INFO:   Iteration 46/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.633s.
INFO:   Estimated completion in 0:00:02.676619, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.457739).
INFO:   ********************************************************************************
INFO:   Iteration 47/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.634s.
INFO:   Estimated completion in 0:00:02.005958, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.432633).
INFO:   ********************************************************************************
INFO:   Iteration 48/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.629s.
INFO:   Estimated completion in 0:00:01.336105, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.402624).
INFO:   ********************************************************************************
INFO:   Iteration 49/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.631s.
INFO:   Estimated completion in 0:00:00.667531, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.376532).
INFO:   ********************************************************************************
INFO:   Iteration 50/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.637s.
INFO:   Estimated completion in 0:00:00, at 2023-Jun-19-21:32:29 (consuming total wall clock time 0:00:33.363456).
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases
INFO:   creating hybrid system
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   Generating a residue template for [H][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] using openff-2.0.0
INFO:   Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>
INFO:   Generating a residue template for [H][O][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] using openff-2.0.0
INFO:   creating hybrid system
INFO:   setting force field terms
INFO:   adding forces
INFO:   DONE
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases
INFO:   minimizing systems

Please cite the following:

        Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209
        Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27
        Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413
        Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w
        Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669


INFO:   equilibrating systems
INFO:   Equilibration iteration 1/10
INFO:   Iteration took 0.879s.
INFO:   Estimated completion (of equilibration only) in 0:00:07.936918, at Mon Jun 19 21:32:56 2023 (consuming total wall clock time 0:00:08.818798).
INFO:   Equilibration iteration 2/10
INFO:   Iteration took 0.611s.
INFO:   Estimated completion (of equilibration only) in 0:00:05.992730, at Mon Jun 19 21:32:55 2023 (consuming total wall clock time 0:00:07.490913).
INFO:   Equilibration iteration 3/10
INFO:   Iteration took 0.619s.
INFO:   Estimated completion (of equilibration only) in 0:00:04.959390, at Mon Jun 19 21:32:55 2023 (consuming total wall clock time 0:00:07.084843).
INFO:   Equilibration iteration 4/10
INFO:   Iteration took 0.623s.
INFO:   Estimated completion (of equilibration only) in 0:00:04.133254, at Mon Jun 19 21:32:54 2023 (consuming total wall clock time 0:00:06.888757).
INFO:   Equilibration iteration 5/10
INFO:   Iteration took 0.626s.
INFO:   Estimated completion (of equilibration only) in 0:00:03.390757, at Mon Jun 19 21:32:54 2023 (consuming total wall clock time 0:00:06.781513).
INFO:   Equilibration iteration 6/10
INFO:   Iteration took 0.623s.
INFO:   Estimated completion (of equilibration only) in 0:00:02.679125, at Mon Jun 19 21:32:54 2023 (consuming total wall clock time 0:00:06.697813).
INFO:   Equilibration iteration 7/10
INFO:   Iteration took 0.622s.
INFO:   Estimated completion (of equilibration only) in 0:00:01.992479, at Mon Jun 19 21:32:54 2023 (consuming total wall clock time 0:00:06.641597).
INFO:   Equilibration iteration 8/10
INFO:   Iteration took 0.661s.
INFO:   Estimated completion (of equilibration only) in 0:00:01.328947, at Mon Jun 19 21:32:54 2023 (consuming total wall clock time 0:00:06.644737).
INFO:   Equilibration iteration 9/10
INFO:   Iteration took 0.675s.
INFO:   Estimated completion (of equilibration only) in 0:00:00.666864, at Mon Jun 19 21:32:54 2023 (consuming total wall clock time 0:00:06.668636).
INFO:   Equilibration iteration 10/10
INFO:   Iteration took 0.688s.
INFO:   Estimated completion (of equilibration only) in 0:00:00, at Mon Jun 19 21:32:54 2023 (consuming total wall clock time 0:00:06.700182).
INFO:   running production phase
INFO:   ********************************************************************************
INFO:   Iteration 1/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.722s.
INFO:   Estimated completion in 0:00:35.757886, at 2023-Jun-19-21:33:31 (consuming total wall clock time 0:00:36.487639).
INFO:   ********************************************************************************
INFO:   Iteration 2/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.686s.
INFO:   Estimated completion in 0:00:34.246227, at 2023-Jun-19-21:33:30 (consuming total wall clock time 0:00:35.673153).
INFO:   ********************************************************************************
INFO:   Iteration 3/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.692s.
INFO:   Estimated completion in 0:00:33.426404, at 2023-Jun-19-21:33:30 (consuming total wall clock time 0:00:35.560004).
INFO:   ********************************************************************************
INFO:   Iteration 4/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.693s.
INFO:   Estimated completion in 0:00:32.654060, at 2023-Jun-19-21:33:30 (consuming total wall clock time 0:00:35.493544).
INFO:   ********************************************************************************
INFO:   Iteration 5/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.697s.
INFO:   Estimated completion in 0:00:31.980154, at 2023-Jun-19-21:33:30 (consuming total wall clock time 0:00:35.533504).
INFO:   ********************************************************************************
INFO:   Iteration 6/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.687s.
INFO:   Estimated completion in 0:00:31.218393, at 2023-Jun-19-21:33:30 (consuming total wall clock time 0:00:35.475447).
INFO:   ********************************************************************************
INFO:   Iteration 7/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.695s.
INFO:   Estimated completion in 0:00:30.504003, at 2023-Jun-19-21:33:30 (consuming total wall clock time 0:00:35.469770).
INFO:   ********************************************************************************
INFO:   Iteration 8/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.696s.
INFO:   Estimated completion in 0:00:29.801046, at 2023-Jun-19-21:33:30 (consuming total wall clock time 0:00:35.477436).
INFO:   ********************************************************************************
INFO:   Iteration 9/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.685s.
INFO:   Estimated completion in 0:00:29.052087, at 2023-Jun-19-21:33:30 (consuming total wall clock time 0:00:35.429374).
INFO:   ********************************************************************************
INFO:   Iteration 10/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.697s.
INFO:   Estimated completion in 0:00:28.358094, at 2023-Jun-19-21:33:30 (consuming total wall clock time 0:00:35.447618).
INFO:   ********************************************************************************
INFO:   Iteration 11/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.705s.
INFO:   Estimated completion in 0:00:27.692122, at 2023-Jun-19-21:33:30 (consuming total wall clock time 0:00:35.502721).
INFO:   ********************************************************************************
INFO:   Iteration 12/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.703s.
INFO:   Estimated completion in 0:00:27.008300, at 2023-Jun-19-21:33:30 (consuming total wall clock time 0:00:35.537237).
INFO:   ********************************************************************************
INFO:   Iteration 13/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.704s.
INFO:   Estimated completion in 0:00:26.325316, at 2023-Jun-19-21:33:30 (consuming total wall clock time 0:00:35.574751).
INFO:   ********************************************************************************
INFO:   Iteration 14/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.711s.
INFO:   Estimated completion in 0:00:25.644808, at 2023-Jun-19-21:33:30 (consuming total wall clock time 0:00:35.617788).
INFO:   ********************************************************************************
INFO:   Iteration 15/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.654s.
INFO:   Estimated completion in 0:00:24.828502, at 2023-Jun-19-21:33:30 (consuming total wall clock time 0:00:35.469289).
INFO:   ********************************************************************************
INFO:   Iteration 16/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.633s.
INFO:   Estimated completion in 0:00:23.982507, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:35.268392).
INFO:   ********************************************************************************
INFO:   Iteration 17/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.636s.
INFO:   Estimated completion in 0:00:23.160323, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:35.091398).
INFO:   ********************************************************************************
INFO:   Iteration 18/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.635s.
INFO:   Estimated completion in 0:00:22.361261, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.939471).
INFO:   ********************************************************************************
INFO:   Iteration 19/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.637s.
INFO:   Estimated completion in 0:00:21.582055, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.809766).
INFO:   ********************************************************************************
INFO:   Iteration 20/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.635s.
INFO:   Estimated completion in 0:00:20.806256, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.677093).
INFO:   ********************************************************************************
INFO:   Iteration 21/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.636s.
INFO:   Estimated completion in 0:00:20.052668, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.573565).
INFO:   ********************************************************************************
INFO:   Iteration 22/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.632s.
INFO:   Estimated completion in 0:00:19.303035, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.469705).
INFO:   ********************************************************************************
INFO:   Iteration 23/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.633s.
INFO:   Estimated completion in 0:00:18.561316, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.372807).
INFO:   ********************************************************************************
INFO:   Iteration 24/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.631s.
INFO:   Estimated completion in 0:00:17.825707, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.280206).
INFO:   ********************************************************************************
INFO:   Iteration 25/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.632s.
INFO:   Estimated completion in 0:00:17.102039, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:34.204077).
INFO:   ********************************************************************************
INFO:   Iteration 26/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.636s.
INFO:   Estimated completion in 0:00:16.383893, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:34.133111).
INFO:   ********************************************************************************
INFO:   Iteration 27/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.633s.
INFO:   Estimated completion in 0:00:15.666444, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:34.057487).
INFO:   ********************************************************************************
INFO:   Iteration 28/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.635s.
INFO:   Estimated completion in 0:00:14.959206, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:33.998196).
INFO:   ********************************************************************************
INFO:   Iteration 29/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.633s.
INFO:   Estimated completion in 0:00:14.256236, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:33.943419).
INFO:   ********************************************************************************
INFO:   Iteration 30/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.666s.
INFO:   Estimated completion in 0:00:13.580158, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:33.950394).
INFO:   ********************************************************************************
INFO:   Iteration 31/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.687s.
INFO:   Estimated completion in 0:00:12.915132, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:33.987189).
INFO:   ********************************************************************************
INFO:   Iteration 32/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.675s.
INFO:   Estimated completion in 0:00:12.241341, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:34.003726).
INFO:   ********************************************************************************
INFO:   Iteration 33/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.703s.
INFO:   Estimated completion in 0:00:11.578899, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:34.055586).
INFO:   ********************************************************************************
INFO:   Iteration 34/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.691s.
INFO:   Estimated completion in 0:00:10.907978, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:34.087430).
INFO:   ********************************************************************************
INFO:   Iteration 35/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.690s.
INFO:   Estimated completion in 0:00:10.235181, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:34.117270).
INFO:   ********************************************************************************
INFO:   Iteration 36/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.689s.
INFO:   Estimated completion in 0:00:09.559187, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:34.139953).
INFO:   ********************************************************************************
INFO:   Iteration 37/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.688s.
INFO:   Estimated completion in 0:00:08.883698, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:34.168068).
INFO:   ********************************************************************************
INFO:   Iteration 38/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.697s.
INFO:   Estimated completion in 0:00:08.208529, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:34.202203).
INFO:   ********************************************************************************
INFO:   Iteration 39/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.697s.
INFO:   Estimated completion in 0:00:07.530735, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:34.230612).
INFO:   ********************************************************************************
INFO:   Iteration 40/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.697s.
INFO:   Estimated completion in 0:00:06.852917, at 2023-Jun-19-21:33:28 (consuming total wall clock time 0:00:34.264584).
INFO:   ********************************************************************************
INFO:   Iteration 41/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.702s.
INFO:   Estimated completion in 0:00:06.174742, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.304123).
INFO:   ********************************************************************************
INFO:   Iteration 42/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.685s.
INFO:   Estimated completion in 0:00:05.490896, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.318099).
INFO:   ********************************************************************************
INFO:   Iteration 43/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.688s.
INFO:   Estimated completion in 0:00:04.806425, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.331608).
INFO:   ********************************************************************************
INFO:   Iteration 44/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.694s.
INFO:   Estimated completion in 0:00:04.122803, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.356691).
INFO:   ********************************************************************************
INFO:   Iteration 45/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.684s.
INFO:   Estimated completion in 0:00:03.436735, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.367352).
INFO:   ********************************************************************************
INFO:   Iteration 46/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.700s.
INFO:   Estimated completion in 0:00:02.751464, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.393304).
INFO:   ********************************************************************************
INFO:   Iteration 47/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.717s.
INFO:   Estimated completion in 0:00:02.066107, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.435114).
INFO:   ********************************************************************************
INFO:   Iteration 48/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.640s.
INFO:   Estimated completion in 0:00:01.375984, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.399595).
INFO:   ********************************************************************************
INFO:   Iteration 49/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.629s.
INFO:   Estimated completion in 0:00:00.687077, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.353854).
INFO:   ********************************************************************************
INFO:   Iteration 50/50
INFO:   ********************************************************************************
INFO:   Iteration took 0.634s.
INFO:   Estimated completion in 0:00:00, at 2023-Jun-19-21:33:29 (consuming total wall clock time 0:00:34.309411).
WARNING:        Warning: The openmmtools.multistate API is experimental and may change in future releases

4. Analysis#

Finally now that we’ve run our simulations, let’s go ahead and gather the free energies for both phases.

This can be achieved by passing the results of executing the DAGs calling the gather() methods of RelativeLigandTransform. This takes a list of completed DAG results, catering for when simulations have been extended.

[39]:

# Get the complex and solvent results
complex_results = rbfe_transform.gather([complex_dag_results])
solvent_results = rbfe_transform.gather([solvent_dag_results])

print(f"Complex dG: {complex_results.get_estimate()}, err {complex_results.get_uncertainty()}")
print(f"Solvent dG: {solvent_results.get_estimate()}, err {solvent_results.get_uncertainty()}")

Complex dG: 3.8428725693840384 kilocalorie / mole, err 0.21918456914295942 kilocalorie / mole
Solvent dG: 1.206767244454323 kilocalorie / mole, err 0.32073333466272824 kilocalorie / mole