Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?

ABSTRACT: Computational chemistry is an important tool in numerous scientific disciplines, including drug discovery and structural biology. Coarse-grained models offer simple representations of molecular systems that enable simulations of large-scale systems. Because there has been an increase in the adoption of such models for simulations of biomolecular systems, critical evaluation is warranted. Here, the stability of the amyloid peptide and organic crystals is evaluated using the Martini 3 coarse-grained force field. The crystals change shape drastically during the simulations. Radial distribution functions show that the distance between backbone beads in β-sheets increases by ∼1 Å, breaking the crystals. The melting points of organic compounds are much too low in the Martini force field. This su

SUBMITTER: Hosseini AN 

PROVIDER: S-EPMC10839907 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature