OpenFE icon

OpenFE

(1.0.0)

Absolute hydration free energy calculations for neutral small molecules Learn more

What is OpenFE?

OpenFE (Open Free Energy) is an open-source Python framework for alchemical free energy calculations, a physics-based computational method used in drug discovery to predict how strongly molecules interact with their environment or a protein target. Rather than scoring a single static pose like molecular docking, alchemical methods simulate the thermodynamics of molecular transformations, yielding quantitative binding affinity estimates in kcal/mol with statistical uncertainty.

This OpenFE run calculates Absolute Hydration Free Energy (AHFE): the free energy change when a neutral small molecule is transferred from vacuum into water. AHFE quantifies how much a compound prefers aqueous solution over the gas phase, a property linked to solubility and membrane permeability.

OpenFE is developed by a consortium of pharmaceutical companies and academic groups, with GPU-accelerated simulations powered by OpenMM.

How alchemical free energy calculations work

In classical thermodynamics, measuring a binding free energy directly would require simulating the full association and dissociation of a ligand, an event that happens on timescales far beyond what molecular dynamics can reach. Alchemical methods sidestep this by exploiting the fact that free energy is a state function: the path between two states does not matter, only the endpoints.

Instead of physically pulling a ligand out of a binding pocket, the calculation gradually "switches off" the ligand's interactions with its surroundings through a series of unphysical intermediate states. A coupling parameter λ\lambdaλ controls this transformation, varying from 0 (full interactions) to 1 (fully decoupled). At each λ\lambdaλ value, a short molecular dynamics simulation samples the local thermodynamics.

Lambda windows

The number of λ\lambdaλ intermediates is called the lambda window count. More windows provide smoother overlap between adjacent states and more reliable free energy estimates, at the cost of additional simulation time.

AHFE thermodynamic cycle

For hydration free energies, the ligand is decoupled in two environments independently:

  1. In solvent: electrostatic interactions are annihilated, then van der Waals interactions are decoupled
  2. In vacuum: the same decoupling is performed without solvent

The hydration free energy is the difference: ΔGhydration=ΔGsolvent−ΔGvacuum\Delta G_{\text{hydration}} = \Delta G_{\text{solvent}} - \Delta G_{\text{vacuum}}ΔGhydration​=ΔGsolvent​−ΔGvacuum​.

Analysis

Free energies are extracted from the simulation data using MBAR (Multistate Bennett Acceptance Ratio), which simultaneously analyzes energy differences across all λ\lambdaλ windows for statistically optimal estimates.

How to use OpenFE online

ProteinIQ provides cloud-hosted OpenFE calculations on GPU infrastructure, handling all environment setup, force field parameterization, and simulation orchestration automatically.

Inputs

InputDescription
LigandSMILES string or SDF file describing one neutral small molecule.

Charged ligands are not supported by OpenFE’s absolute-solvation protocol.

Calculation settings

SettingDescription
Simulation LengthDuration per lambda window. Production uses OpenFE’s default 10 ns solvent and 2 ns vacuum sampling; shorter profiles are exploratory.
Number of RepeatsIndependent repeat calculations. 3 is the OpenFE default and supports a repeat-based uncertainty estimate.

Advanced settings

SettingDescription
Water modelTIP3P (fast, well-validated) or TIP4P-Ew (more accurate solvation thermodynamics, slower).

Results

Results include the hydration free energy estimate, statistical uncertainty, per-leg and per-repeat estimates, and downloadable OpenFE run artifacts for inspection.

Interpreting results

AHFE values

Hydration free energies are typically negative for polar, water-soluble compounds and near zero or positive for hydrophobic molecules. Experimental AHFE values for druglike molecules generally range from +2+2+2 to −15-15−15 kcal/mol. Well-converged OpenFE AHFE calculations typically achieve accuracy within 1 kcal/mol of experimental values.

Uncertainty and convergence

Results include statistical uncertainty from MBAR analysis. If uncertainty exceeds 1 kcal/mol, the calculation may not be converged. Increasing simulation length or running more repeats can improve convergence.

Limitations

  • Neutral molecules only: The OpenFE absolute-solvation protocol does not support charged alchemical molecules.
  • Force field dependence: Results are only as accurate as the underlying force field. Molecules with unusual functional groups may be poorly parameterized.
  • Convergence is not guaranteed: Short simulations with few lambda windows can produce results with small reported uncertainties that are nonetheless systematically wrong. When accuracy matters, use longer simulations with 3 repeats.

Table of contents

OpenFE icon

OpenFE

(1.0.0)

Absolute hydration free energy calculations for neutral small molecules Learn more

What is OpenFE?

OpenFE (Open Free Energy) is an open-source Python framework for alchemical free energy calculations, a physics-based computational method used in drug discovery to predict how strongly molecules interact with their environment or a protein target. Rather than scoring a single static pose like molecular docking, alchemical methods simulate the thermodynamics of molecular transformations, yielding quantitative binding affinity estimates in kcal/mol with statistical uncertainty.

This OpenFE run calculates Absolute Hydration Free Energy (AHFE): the free energy change when a neutral small molecule is transferred from vacuum into water. AHFE quantifies how much a compound prefers aqueous solution over the gas phase, a property linked to solubility and membrane permeability.

OpenFE is developed by a consortium of pharmaceutical companies and academic groups, with GPU-accelerated simulations powered by OpenMM.

How alchemical free energy calculations work

In classical thermodynamics, measuring a binding free energy directly would require simulating the full association and dissociation of a ligand, an event that happens on timescales far beyond what molecular dynamics can reach. Alchemical methods sidestep this by exploiting the fact that free energy is a state function: the path between two states does not matter, only the endpoints.

Instead of physically pulling a ligand out of a binding pocket, the calculation gradually "switches off" the ligand's interactions with its surroundings through a series of unphysical intermediate states. A coupling parameter λ\lambdaλ controls this transformation, varying from 0 (full interactions) to 1 (fully decoupled). At each λ\lambdaλ value, a short molecular dynamics simulation samples the local thermodynamics.

Lambda windows

The number of λ\lambdaλ intermediates is called the lambda window count. More windows provide smoother overlap between adjacent states and more reliable free energy estimates, at the cost of additional simulation time.

AHFE thermodynamic cycle

For hydration free energies, the ligand is decoupled in two environments independently:

  1. In solvent: electrostatic interactions are annihilated, then van der Waals interactions are decoupled
  2. In vacuum: the same decoupling is performed without solvent

The hydration free energy is the difference: ΔGhydration=ΔGsolvent−ΔGvacuum\Delta G_{\text{hydration}} = \Delta G_{\text{solvent}} - \Delta G_{\text{vacuum}}ΔGhydration​=ΔGsolvent​−ΔGvacuum​.

Analysis

Free energies are extracted from the simulation data using MBAR (Multistate Bennett Acceptance Ratio), which simultaneously analyzes energy differences across all λ\lambdaλ windows for statistically optimal estimates.

How to use OpenFE online

ProteinIQ provides cloud-hosted OpenFE calculations on GPU infrastructure, handling all environment setup, force field parameterization, and simulation orchestration automatically.

Inputs

InputDescription
LigandSMILES string or SDF file describing one neutral small molecule.

Charged ligands are not supported by OpenFE’s absolute-solvation protocol.

Calculation settings

SettingDescription
Simulation LengthDuration per lambda window. Production uses OpenFE’s default 10 ns solvent and 2 ns vacuum sampling; shorter profiles are exploratory.
Number of RepeatsIndependent repeat calculations. 3 is the OpenFE default and supports a repeat-based uncertainty estimate.

Advanced settings

SettingDescription
Water modelTIP3P (fast, well-validated) or TIP4P-Ew (more accurate solvation thermodynamics, slower).

Results

Results include the hydration free energy estimate, statistical uncertainty, per-leg and per-repeat estimates, and downloadable OpenFE run artifacts for inspection.

Interpreting results

AHFE values

Hydration free energies are typically negative for polar, water-soluble compounds and near zero or positive for hydrophobic molecules. Experimental AHFE values for druglike molecules generally range from +2+2+2 to −15-15−15 kcal/mol. Well-converged OpenFE AHFE calculations typically achieve accuracy within 1 kcal/mol of experimental values.

Uncertainty and convergence

Results include statistical uncertainty from MBAR analysis. If uncertainty exceeds 1 kcal/mol, the calculation may not be converged. Increasing simulation length or running more repeats can improve convergence.

Limitations

  • Neutral molecules only: The OpenFE absolute-solvation protocol does not support charged alchemical molecules.
  • Force field dependence: Results are only as accurate as the underlying force field. Molecules with unusual functional groups may be poorly parameterized.
  • Convergence is not guaranteed: Short simulations with few lambda windows can produce results with small reported uncertainties that are nonetheless systematically wrong. When accuracy matters, use longer simulations with 3 repeats.

Table of contents

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