ABsolute SOLVantion Free Energy Calculations
The absolv framework aims to offer a simple API for computing the change in free energy when transferring a solute from one solvent to another, or to vacuum in the case of solvation free energy calculations.
It offers two routes to this end: standard equilibrium calculations and non-equilibrium switching type calculations, where the latter is the main focus of this framework.
Warning: This code is currently experimental and under active development. If you are using this it, please be aware that it is not guaranteed to provide correct results, the documentation and testing is incomplete, and the API can change without notice.
Installation
The core dependencies can be installed using the conda package manager:
conda env create --name absolv --file devtools/conda-envs/test-env.yaml
python setup.py develop
Getting Started
To begin with we define a schema that will, for all intents and purposes, encode the entirety of the absolute free energy calculation that we will be running.
In particular, we must specify:
i) the solutes and the two solvents that they will be transferred between ii) the state, i.e. temperature and optionally pressure, to perform the calculation at iii) and finally, the type of free energy calculation to perform as well as the protocol to follow while perform it
This can be compactly done by creating a new TransferFreeEnergySchema object:
from absolv.models import EquilibriumProtocol, State, System, TransferFreeEnergySchema
schema = TransferFreeEnergySchema(
# Define the solutes in the system. There may be multiple in the case of,
# e.g., ion pairs like Na+ + Cl-. Here we use `None` to specify that the solute
# will be transferred into a vacuum.
system=System(solutes={"CCO": 1}, solvent_a={"O": 895}, solvent_b=None),
# Define the state that the calculation will be performed at.
state=State(temperature=298.15, pressure=1.0),
# Define the alchemical pathway to transform the solute along in the first
# and second (i.e. vacuum) solvent respectively.
alchemical_protocol_a=EquilibriumProtocol(
lambda_sterics=[ # fmt: off
1.00, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.80, 0.70, 0.60, 0.50, 0.40,
0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00,
],
lambda_electrostatics=[ # fmt: off
1.00, 0.75, 0.50, 0.25, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00,
0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00,
],
),
alchemical_protocol_b=EquilibriumProtocol(
lambda_sterics=[1.0, 1.0, 1.0, 1.0, 1.0],
lambda_electrostatics=[1.0, 0.75, 0.5, 0.25, 0.0],
),
)
Here we have specified that we will be computing the solvation free energy of one ethanol molecule in 895 water molecules at a temperature and pressure of 298.15 K and 1 atm.
We have also specified that we will be performing a standard 'equilibrium' free energy calculation according to the paper described by Mobley et al [1].
We can then trivially set up,
from openff.toolkit.typing.engines.smirnoff import ForceField
force_field = ForceField("openff-2.0.0.offxml")
from absolv.runners.equilibrium import EquilibriumRunner
EquilibriumRunner.setup(schema, force_field)
run,
EquilibriumRunner.run(schema, platform="CUDA")
and analyze the calculations
free_energies = EquilibriumRunner.analyze(schema)
print(free_energies)
Theory
...
Equilibrium Calculations
...
Non-equilibrium Calculations
...
Alchemical Transformations
...
Electrostatics
...
LJ Soft Core
...
Custom vdW Forms
...
References
[1] Mobley, David L., et al. "Escaping atom types in force fields using direct chemical perception." Journal of chemical theory and computation 14.11 (2018): 6076-6092.
License
The main package is release under the MIT license.
Copyright
Copyright (c) 2021, Simon Boothroyd
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