Model-free simulation approach to molecular diffusion tensors.

Area of Science:

• Computational Chemistry
• Molecular Dynamics Simulations
• Physical Chemistry

Background:

• Accurate calculation of molecular diffusion tensors is crucial for understanding molecular behavior in condensed phases.
• Existing methods may require complex models or extensive computational resources.

Purpose of the Study:

• To develop a simple, model-free approach for computing molecular diffusion tensors.
• To enable accurate analysis of molecular dynamics trajectories for diffusion properties.

Main Methods:

• A rigid body trajectory is constructed from molecular dynamics data using quaternion-based superposition fits.
• Translational and angular velocities are computed, and angular trajectories are integrated.
• The diffusion tensor is calculated from the mean square displacement and Kubo integral.

Main Results:

• The proposed method successfully computes molecular diffusion tensors for water and lysozyme molecules.
• Estimations of statistical accuracy for the calculations are provided.
• The approach is validated using both mean square displacement and Kubo integral methods.

Conclusions:

• The developed model-free approach offers a computationally efficient and accurate way to determine molecular diffusion tensors.
• This method enhances the analysis of molecular dynamics simulations for studying molecular transport phenomena.