CHARMM-GUI Nanomaterial Modeler: extension to ligand-protected nanomaterials

Functionalized nanoparticles and surfaces are at the forefront of nanoscience. They hold the promise of innovative applications for human health and technology. In this context, molecular dynamics (MD) simulations are increasingly employed to understand the fundamental structural and dynamical features of functionalized nanomaterials. However, such simulations demand a laborious process, such as i) construction of complex 3D models of nanomaterials and its functionalization with organic ligands and ii) correct assignment of force-field parameters to the composite systems.