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Jul 2026

Efficient Force Evaluation via Fragmentation: Toward Geometry Optimization of Protein-Ligand Systems with Quantum Mechanical Accuracy.

This work presents a hybrid fragmentation-based approach, FragQMMM, that enables efficient and accurate force evaluation for large molecular systems, and successfully reproduces the hydrogen-bond network and preserving the underlying structure-activity relationship.

R. Han, Zonghua Bo, Jiawei Yan · 0 citations
Open access Aug 2026

Fast intermolecular interaction energy calculation with the OPLS-AA force field

A fast pipeline based on the OPLS-AA force field is presented that enables the automated calculation of non-bonding intermolecular (dimer) interaction energies derived from a set of small organic (monomer) molecules. To calculate the non-bonding contributions, optimized geometries of the monomer molecules as well as their OPLS-AA van der Waals and atomic partial charge parameters are required. The key advantage of the new pipeline lies in its fast, highly parallelized in-memory computations without slow I/O operations, which make it possible to thoroughly process comparatively large numbers of (more than a hundred) monomer molecules within acceptable time frames (hours and days): Compared to an analogous, more versatile, and comprehensive approach, the new computational scheme delivers comparable results while being more than two orders of magnitude faster. For locally estimating the required OPLS-AA force field parameters with the LigParGen and BOSS software packages, a user-friendly graphical user interface for the Windows operating system is provided. Scientific contribution Rapid calculation of mutual intermolecular energies for a set of monomer molecules based on the widely used OPLS-AA force field enables a considerable expansion of this type of calculation for practical purposes. The performance improvement can be used to achieve significant improvements of interaction energy averages as well as considerable expansions in the size of the monomer molecule set.

Mirco Daniel, Hannah Kullik, Martin Urban et al. · 0 citations
Jul 2026

A refined general AMBER force field for liquid acetonitrile: Development and validation.

GAFF-ACN, a refined general AMBER force field specific for liquid acetonitrile, is introduced aiming for accurately reproducing both the experimental density and static dielectric constant using classical NPT molecular dynamics (MD) simulations. Its parameterization combines a quantum-mechanically derived geometry with restrained electrostatic potential charges in a polarizable continuum model, standard GAFFv2.11 parameters, and enforced molecular linearity. GAFF-ACN reproduces a broad set of macroscopic and microscopic properties of liquid acetonitrile. The density agrees closely with experiment (-0.4% relative error), and the static dielectric constant differs by 13%, representing, to the best of our knowledge, the most accurate dielectric constant reported to date for a fixed-charge model. GAFF-ACN also reproduces (i) key thermodynamic observables, i.e., heat of vaporization, surface tension, isothermal compressibility, and thermal expansion coefficient; (ii) mass transport coefficients, viz. self-diffusion and shear viscosity; and (iii) structural aspects including pairwise radial distribution functions and coordination numbers. All results are obtained using standard simulation protocols, enabling reproducibility and straightforward adoption across common MD packages. GAFF-ACN, therefore, provides an accurate and practical acetonitrile model for the solvation of GAFF-parameterized organic solutes.

Noah Deveaux, Benoît Champagne, Tárcius N. Ramos · 0 citations
Review Jul 2026

CP2K: An electronic structure and molecular dynamics software package - Dynamics, Transport, and Spectroscopic Response

One of the distinguishing aspects of CP2K is its seamless integration of diverse structural and transition-state optimization techniques with advanced sampling approaches including Monte Carlo, molecular dynamics, and metadynamics, enabling the efficient exploration of complex potential- and free-energy landscapes, including rare events. These capabilities are combined with a broad hierarchy of energy and force evaluation methods, ranging from classical and machine-learned interaction potentials and mixed quantum-classical multiscale and semiempirical schemes, to highly accurate quantum-mechanical electronic-structure approaches. At the heart of the latter lies the Gaussian and plane-wave framework, along with its augmented all-electron generalization, which have been described in detail in our previous code review [T. D. K\"uhne et al., J. Chem. Phys. 152, 194103 (2020)]. Building on this foundation, the present work revisits the methods within CP2K that turn electronic structure into dynamics, transport, and spectroscopic response. Particular emphasis is placed on the coupling between static response calculations and nuclear motion: spectra may be evaluated at optimized structures, averaged over thermally sampled configurations, obtained from time-correlation functions along ab-initio or path integral molecular trajectories, or followed in real time together with electronic and nuclear dynamics. The same modular structure also enables equilibrium and biased transport simulations, from Kubo-type linear response to open-boundary approaches under external potentials, highlighting CP2K's unique capability to unify quantum chemistry with quantum and statistical mechanics within a versatile, holistic simulation environment.

Jan Wilhelm, Anna-Sophia Hehn, Hossam Elgabarty et al. · 1 citation · ⚡1
Preprint Jul 2026

Quantum Computing Enabled ab initio Molecular Dynamics Simulations

We demonstrate a quantum-classical workflow for ab initio molecular dynamics (AIMD) in which quantum measurements from a chemistry-inspired LUCJ ansatz are post-processed using Sample-based Quantum Diagonalization (SQD) to recover determinant subspaces and deliver energies and analytical nuclear gradients for dynamics. As an exact benchmark, we use full configuration interaction (FCI) in the STO-3G basis, enabling a direct assessment of the accuracy of SQD. In gas-phase benchmarks, SQD reproduces FCI energies and gradients to within 1 kcal mol$^{-1}$ of the FCI reference and yields stable AIMD trajectories. In explicit-solvent QM/MM simulations, SQD retains this agreement, matching FCI energy fluctuations and RMS gradient profiles and reproducing solute-solvent structure as quantified by radial distribution functions. Overall, these benchmarks establish LUCJ+SQD as a practical route for integrating current quantum hardware into QM/MM molecular dynamics and provide an early demonstration of condensed-phase QM/MM dynamics driven by a quantum electronic-structure engine.

Susanta Das, Subhamoy Bhowmik, Zhen Li et al. · 0 citations
Aug 2026

Fast-Forward: Automatic Assignment and Assessment of Bonded Parameters for the Martini Force Field

Coarse-grained molecular dynamics simulations of bio- and macromolecular systems offer a method of accessing otherwise unobtainable time and length scales, compared to atomistic simulation techniques. However, a limiting step is often the generation and validation of the coarse-grained models. Here, we describe a new software package, Fast-Forward, which aids parametrization of models for the widely used Martini coarse-grained force field. In comparison to other similar packages, Fast-Forward offers a system-agnostic suite of tools to parametrize molecules of any size, existing in any environment. It achieves this while maintaining ease of use and the use of interoperable file formats from the Martini software ecosystem. Through its three subprograms, the package offers tools for trajectory mapping, parameter generation, and model validation. We demonstrate the potential of the package for several different use cases, from small biological molecules (glutathione and glutathione disulfide) to models of synthetic polymers (poly(methyl methacrylate), PMMA).

Christopher Brasnett, Maximilian Fidlin, Thilo Duve et al. · 0 citations