An imbalance in the force: the need for standardized benchmarks for molecular simulation

K Kriz, L Schmidt, AT Andersson, MM Walz… - Journal of Chemical …, 2023 - ACS Publications
Force fields (FFs) for molecular simulation have been under development for more than half
a century. As with any predictive model, rigorous testing and comparisons of models …

Martini on the rocks: can a coarse-grained force field model crystals?

AN Hosseini, D van der Spoel - The Journal of Physical Chemistry …, 2024 - ACS Publications
Computational chemistry is an important tool in numerous scientific disciplines, including
drug discovery and structural biology. Coarse-grained models offer simple representations …

Template-Directed In Crystallo Photopolymerization of a Donor–Acceptor Cyclopropane: When Everything Falls into Place!

M Giorgi, K Masson, S Chentouf… - Journal of the …, 2024 - ACS Publications
A single-crystal-to-single-crystal solid-state reaction of vinylogous donor–acceptor
cyclopropanes is documented. The enantiospecific synthesis of new products, distinct from …

Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas-and Condensed-Phase Properties of Noble Gases

K Kriz, PJ van Maaren… - Journal of Chemical …, 2024 - ACS Publications
The systems of noble gases are particularly instructive for molecular modeling due to the
elemental nature of their interactions. They do not normally form bonds nor possess a …

Quantification of Anisotropy in Exchange and Dispersion Interactions: A Simple Model for Physics-Based Force Fields

K Kříž, D Van der Spoel - The Journal of Physical Chemistry …, 2024 - ACS Publications
In some compounds, exchange repulsion is orientation dependent. However, in contrast to
quantum chemical methods that treat exchange explicitly, empirical models assume …

gmXtal: Cooking crystals with GROMACS

P Buslaev, G Groenhof - The Protein Journal, 2024 - Springer
Molecular dynamics (MD) simulations are routinely performed of biomolecules in solution,
because this is their native environment. However, the structures used in such simulations …

Simulations of Amyloid-Forming Peptides in the Crystal State

AN Hosseini, D Van der Spoel - The Protein Journal, 2023 - Springer
There still is little treatment available for amyloid diseases, despite their significant impact on
individuals and the social and economic implications for society. One reason for this is that …

Classical Molecular Dynamics Simulation of Molecular Crystals and Materials: Old Lessons and New Perspectives

G Macetti, L Sironi, L Lo Presti - Chemistry, Molecular Sciences and …, 2023 - air.unimi.it
The basics and state-of-the-art methods for the computer simulation of molecular materials
with classical physics are reviewed. The special features of the Milano Chemistry Molecular …