oxDNA.org

oxDNA.org provides coarse-grained molecular dynamics simulations of DNA and RNA nanostructures using the oxDNA and oxRNA models for prototyping and analyzing nanostructure designs.

Key Features:

• oxDNA and oxRNA models: Implements the oxDNA and oxRNA coarse-grained nucleotide-level models for DNA and RNA nanostructure simulations.
• Automated simulation setup: Automatically generates simulation input files and implements a multi-step relaxation protocol for structures exported in non-physical states.
• Equilibrium sampling: Performs equilibrium sampling of assembled designs to assess structural stability and conformational ensembles.
• GPU-accelerated execution: Executes molecular dynamics simulations on GPU-enabled high-performance computing infrastructure for accelerated sampling.
• Visualization and analysis: Provides trajectory visualization and analysis via oxView for exploration of simulation results.

Scientific Applications:

• Design prototyping: Prototyping and evaluating DNA and RNA nanostructure designs using coarse-grained dynamics.
• Stability assessment: Assessing thermodynamic and structural stability of assembled nanostructures under simulated conditions.
• Design rationalization and optimization: Rationalizing complex nanostructure behavior and informing iterative design optimization.

Methodology:

Coarse-grained molecular dynamics using the oxDNA and oxRNA models; automated generation of simulation input files; multi-step relaxation protocols for non-physical starting states; equilibrium sampling of assembled designs; GPU-accelerated execution; trajectory visualization via oxView.