EspalomaCharge: Machine learning-enabled ultra-fast partial charge assignment
This enables faster and more consistent charge assignment for small molecules and biopolymers, advancing next-generation biomolecular force fields.
The paper tackles the slow speed of assigning atomic partial charges for molecular dynamics simulations by proposing a hybrid graph neural network and physical model approach, achieving orders of magnitude faster computation while maintaining accuracy comparable to existing methods.
Atomic partial charges are crucial parameters in molecular dynamics (MD) simulation, dictating the electrostatic contributions to intermolecular energies, and thereby the potential energy landscape. Traditionally, the assignment of partial charges has relied on surrogates of \textit{ab initio} semiempirical quantum chemical methods such as AM1-BCC, and is expensive for large systems or large numbers of molecules. We propose a hybrid physical / graph neural network-based approximation to the widely popular AM1-BCC charge model that is orders of magnitude faster while maintaining accuracy comparable to differences in AM1-BCC implementations. Our hybrid approach couples a graph neural network to a streamlined charge equilibration approach in order to predict molecule-specific atomic electronegativity and hardness parameters, followed by analytical determination of optimal charge-equilibrated parameters that preserves total molecular charge. This hybrid approach scales linearly with the number of atoms, enabling, for the first time, the use of fully consistent charge models for small molecules and biopolymers for the construction of next-generation self-consistent biomolecular force fields. Implemented in the free and open source package \texttt{espaloma\_charge}, this approach provides drop-in replacements for both AmberTools \texttt{antechamber} and the Open Force Field Toolkit charging workflows, in addition to stand-alone charge generation interfaces. Source code is available at \url{https://github.com/choderalab/espaloma_charge}.