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1. Type Label Framework for Bonded Force Fields in LAMMPS

   https://doi.org/10.1021/acs.jpcb.3c08419  

   Gissinger, Jacob R; Nikiforov, Ilia; Afshar, Yaser; Waters, Brendon; Choi, Moon-ki; Karls, Daniel S; Stukowski, Alexander; Im, Wonpil; Heinz, Hendrik; Kohlmeyer, Axel; et al (April 2024, The Journal of Physical Chemistry B)

   New functionality is added to the LAMMPS molecular simulation package, which increases the versatility with which LAMMPS can interface with supporting software and manipulate information associated with bonded force fields. We introduce the “type label” framework that allows atom types and their higher-order interactions (bonds, angles, dihedrals, and impropers) to be represented in terms of the standard atom type strings of a bonded force field. Type labels increase the human readability of input files, enable bonded force fields to be supported by the OpenKIM repository, simplify the creation of reaction templates for the REACTER protocol, and increase compatibility with external visualization tools, such as VMD and OVITO. An introductory primer on the forms and use of bonded force fields is provided to motivate this new functionality and serve as an entry point for LAMMPS and OpenKIM users unfamiliar with bonded force fields. The type label framework has the potential to streamline modeling workflows that use LAMMPS by increasing the portability of software, files, and scripts for preprocessing, running, and postprocessing a molecular simulation. 

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2. Development of an Advanced Force Field for Water using Variational Energy Decomposition Analysis

   Akshaya K. Das, Lars Urban (January 2019, ArXiv.org)

   Given the piecewise approach to modeling intermolecular interactions for force fields, they can be difficult to parameterize since they are fit to data like total energies that only indirectly connect to their separable functional forms. Furthermore, by neglecting certain types of molecular interactions such as charge penetration and charge transfer, most classical force fields must rely on, but do not always demonstrate, how cancellation of errors occurs among the remaining molecular interactions accounted for such as exchange repulsion, electrostatics, and polarization. In this work we present the first generation of the (many-body) MB-UCB force field that explicitly accounts for the decomposed molecular interactions commensurate with a variational energy decomposition analysis, including charge transfer, with force field design choices that reduce the computational expense of the MB-UCB potential while remaining accurate. We optimize parameters using only single water molecule and water cluster data up through pentamers, with no fitting to condensed phase data, and we demonstrate that high accuracy is maintained when the force field is subsequently validated against conformational energies of larger water cluster data sets, radial distribution functions of the liquid phase, and the temperature dependence of thermodynamic and transport water properties. We conclude that MB-UCB is comparable in performance to MB-Pol, but is less expensive and more transferable by eliminating the need to represent short-ranged interactions through large parameter fits to high order polynomials 

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3. Compliant mechanical response of the ultrafast folding protein EnHD under force

   https://doi.org/10.1038/s42005-022-01125-5  

   Reifs, Antonio; Ruiz Ortiz, Irene; Saa, Amaia Ochandorena; Schönfelder, Jörg; De Sancho, David; Muñoz, Victor; Perez-Jimenez, Raul (December 2023, Communications Physics)

   Abstract Ultrafast folding proteins have become an important paradigm in the study of protein folding dynamics. Due to their low energetic barriers and fast kinetics, they are amenable for study by both experiment and simulation. However, single molecule force spectroscopy experiments on these systems are challenging as these proteins do not provide the mechanical fingerprints characteristic of more mechanically stable proteins, which makes it difficult to extract information about the folding dynamics of the molecule. Here, we investigate the unfolding of the ultrafast protein Engrailed Homeodomain (EnHD) by single-molecule atomic force microscopy experiments. Constant speed experiments on EnHD result in featureless transitions typical of compliant proteins. However, in the force-ramp mode we recover sigmoidal curves that we interpret as a very compliant protein that folds and unfolds many times over a marginal barrier. This is supported by a simple theoretical model and coarse-grained molecular simulations. Our results show the ability of force to modulate the unfolding dynamics of ultrafast folding proteins. 

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4. Universal insertion of molecules in ionic compounds under pressure

   https://doi.org/10.1093/nsr/nwae016  

   Peng, Feng; Ma, Yanming; Pickard, Chris J.; Liu, Hanyu; Miao, Maosheng (January 2024, National Science Review)

   ABSTRACT Using first-principles calculations and crystal structure search methods, we found that many covalently bonded molecules such as H2, N2, CO2, NH3, H2O and CH4 may react with NaCl, a prototype ionic solid, and form stable compounds under pressure while retaining their molecular structure. These molecules, despite whether they are homonuclear or heteronuclear, polar or non-polar, small or large, do not show strong chemical interactions with surrounding Na and Cl ions. In contrast, the most stable molecule among all examples, N2, is found to transform into cyclo-N5− anions while reacting with NaCl under high pressures. It provides a new route to synthesize pentazolates, which are promising green energy materials with high energy density. Our work demonstrates a unique and universal hybridization propensity of covalently bonded molecules and solid compounds under pressure. This surprising miscibility suggests possible mixing regions between the molecular and rock layers in the interiors of large planets. 

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5. How close are the classical two-body potentials to ab initio calculations? Insights from linear machine learning based force matching

   https://doi.org/10.1063/5.0175756  

   Yu, Zheng; Annamareddy, Ajay; Morgan, Dane; Wang, Bu (February 2024, The Journal of Chemical Physics)

   In this work, we propose a linear machine learning force matching approach that can directly extract pair atomic interactions from ab initio calculations in amorphous structures. The local feature representation is specifically chosen to make the linear weights a force field as a force/potential function of the atom pair distance. Consequently, this set of functions is the closest representation of the ab initio forces, given the two-body approximation and finite scanning in the configurational space. We validate this approach in amorphous silica. Potentials in the new force field (consisting of tabulated Si–Si, Si–O, and O–O potentials) are significantly different than existing potentials that are commonly used for silica, even though all of them produce the tetrahedral network structure and roughly similar glass properties. This suggests that the commonly used classical force fields do not offer fundamentally accurate representations of the atomic interaction in silica. The new force field furthermore produces a lower glass transition temperature (Tg ∼ 1800 K) and a positive liquid thermal expansion coefficient, suggesting the extraordinarily high Tg and negative liquid thermal expansion of simulated silica could be artifacts of previously developed classical potentials. Overall, the proposed approach provides a fundamental yet intuitive way to evaluate two-body potentials against ab initio calculations, thereby offering an efficient way to guide the development of classical force fields. 

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