Nanomaterial Modeler

Nanomaterial Modeler generates atomistic nanomaterial models, associated topologies, and simulation input files to enable molecular dynamics investigations of mechanical, physicochemical, thermodynamic, and interfacial properties.

Key Features:

• Integration with CHARMM-GUI: Produces models and simulation inputs within the CHARMM-GUI framework for downstream use in multiple molecular dynamics packages.
• Interface Force Field (IFF): Relies on the interface force field (IFF) to provide transferable parameterization for nanomaterial systems.
• Model and topology generation: Automatically generates diverse nanomaterial models along with corresponding topologies and configuration files for MD simulations.
• Lennard-Jones cutoff methods: Implements three LJ treatments—simple truncation at r = 12 Å (12 cutoff), force-based switching over 10–12 Å (10-12 fsw), and LJ particle mesh Ewald with no cutoff (LJPME).
• Energy validation: Performs single-point energy calculations reporting minimal relative absolute energy differences (0.01%) across diverse surface models and equilibrium nanoparticle shapes.
• Property validation: Validates structural, interfacial, and mechanical properties and compares computed density and surface energies to experimental data.
• Quantified deviations: Reports deviations from experiment for densities (up to 4%) and surface energies (up to 8%), with observed ordering among cutoff methods 10-12 fsw < 12 cutoff < LJPME.
• Complex interface construction: Generates nanomaterial-biomolecule and nanomaterial-polymer interface systems using existing CHARMM-GUI modules.

Scientific Applications:

• Molecular dynamics simulations: Provision of topologies and input files for advanced MD studies across multiple simulation packages.
• Interfacial studies: Analysis of nanomaterial-biomolecule and nanomaterial-polymer interfaces at the molecular level.
• Mechanical property evaluation: Investigation of mechanical properties of nanomaterials via validated simulation setups.
• Physicochemical and thermodynamic analysis: Determination of density, surface energy, and related thermodynamic properties and comparison to experimental values.
• Structural and dynamical characterization: Exploration of structure and dynamics of complex nanomaterial-containing systems.

Methodology:

Uses the interface force field (IFF); generates atomistic models, topologies, and configuration files; performs single-point energy calculations (reporting ~0.01% relative absolute energy differences); evaluates three LJ treatments (12 cutoff, 10-12 fsw, LJPME); validates structural, interfacial, and mechanical properties and compares computed density and surface energies to experimental data; constructs nanomaterial-biomolecule and nanomaterial-polymer systems via CHARMM-GUI modules.