Reactive Martini: Chemical Reactions in Coarse-Grained Molecular Dynamics Simulations.

ABSTRACT: Chemical reactions are ubiquitous in both materials and the biophysical sciences. While coarse-grained (CG) molecular dynamics simulations are often needed to study the spatiotemporal scales present in these fields, chemical reactivity has not been explored thoroughly in CG models. In this work, a new approach to model chemical reactivity is presented for the widely used Martini CG Martini model. Employing tabulated potentials with a single extra particle for the angle dependence, the model provides a generic framework for capturing bonded topology changes using nonbonded interactions. As a first example application, the reactive model is used to study the macrocycle formation of benzene-1,3-dithiol molecules through the formation of disulfide bonds. We show that starting from monomers, ma

SUBMITTER: Sami S 

PROVIDER: S-EPMC10339680 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature