From populations to absolute binding affinities in molecular simulations: exact volumetric terms and practical estimators
Abstract
Biomolecular simulations of binding commonly confine the unbound ligand with volumetric restraints to accelerate convergence. However, a general account of how such restraints enter the volumetric term of the standard binding free energy, and of how this term should be evaluated from histogram data, is currently lacking. We take as our starting point the established relation, in the dilute limit, between the binding constant K and the relative populations of the bound and unbound states, which we re-derive from the canonical partition function of molecular solutes in explicit solvent. Building on this relation, we show that a restraint that leaves the bound state unaffected and confines a homogeneous unbound region modifies the volumetric term in a single way, by replacing the system volume with the volume of the region over which the unbound population is evaluated. This yields closed-form estimators for restrained simulations, computable from histograms of any suitably defined reaction coordinate, with the volumetric term kept explicit. Previous expressions based on the potential of mean force are recovered as a special case. The analysis also exposes two distinct errors in current practice: single-bin estimators, which reduce the bound state to one histogram bin and are not valid estimators of K, and working formulas that omit the bin width entering the volumetric term, which make the result depend on the unit of length. We apply the estimators to a Lennard-Jones dimer, the cucurbit[7]uril/1-adamantanol host--guest complex, and the galactonate--DgoT ligand--protein complex.
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BibTeX
@misc{mandelli2026from,
title = {{From populations to absolute binding affinities in molecular simulations: exact volumetric terms and practical estimators}},
author = {Davide Mandelli and Emiliano Ippoliti and Charles Plate},
howpublished = {arXiv},
year = {2026},
month = nov,
doi = {10.48550/arxiv.2608.04834},
eprint = {2608.04834},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2608.04834},
note = {CC BY 4.0},
}
RIS
TY - UNPB
TI - From populations to absolute binding affinities in molecular simulations: exact volumetric terms and practical estimators
AU - Davide Mandelli
AU - Emiliano Ippoliti
AU - Charles Plate
PY - 2026
DA - 2026/11/07
PB - arXiv
DO - 10.48550/arxiv.2608.04834
UR - https://arxiv.org/abs/2608.04834
AB - Biomolecular simulations of binding commonly confine the unbound ligand with volumetric restraints to accelerate convergence. However, a general account of how such restraints enter the volumetric term of the standard binding free energy, and of how this term should be evaluated from histogram data, is currently lacking. We take as our starting point the established relation, in the dilute limit, between the binding constant K and the relative populations of the bound and unbound states, which we re-derive from the canonical partition function of molecular solutes in explicit solvent. Building on this relation, we show that a restraint that leaves the bound state unaffected and confines a homogeneous unbound region modifies the volumetric term in a single way, by replacing the system volume with the volume of the region over which the unbound population is evaluated. This yields closed-form estimators for restrained simulations, computable from histograms of any suitably defined reaction coordinate, with the volumetric term kept explicit. Previous expressions based on the potential of mean force are recovered as a special case. The analysis also exposes two distinct errors in current practice: single-bin estimators, which reduce the bound state to one histogram bin and are not valid estimators of K, and working formulas that omit the bin width entering the volumetric term, which make the result depend on the unit of length. We apply the estimators to a Lennard-Jones dimer, the cucurbit[7]uril/1-adamantanol host--guest complex, and the galactonate--DgoT ligand--protein complex.
ER -