Local Temperature Measurement in Molecular Dynamics Simulations with Rigid Constraints

Area of Science:

• Computational chemistry
• Molecular dynamics simulations
• Statistical mechanics

Background:

• Molecular simulations often use constraints (e.g., fixed bond lengths) to reduce computational cost.
• These constraints alter the system's degrees of freedom (DoF), impacting temperature calculations.
• Incorrect DoF calculation can lead to unphysical violation of kinetic energy equipartition.

Purpose of the Study:

• To develop a method for accurately calculating local temperatures in molecular simulations with arbitrary geometric constraints.
• To self-consistently evaluate the degrees of freedom (DoF) of constrained atoms for correct temperature determination.
• To provide a reliable method for assessing the validity of kinetic energy equipartition in simulations.

Main Methods:

• Developed a self-consistent approach to evaluate degrees of freedom (DoF) for atoms under general geometric constraints.
• Calculated local temperatures from arbitrary Cartesian component kinetic energies.
• Validated the method on diverse systems, including those with temperature gradients and confined geometries.

Main Results:

• The method accurately calculates local temperatures by correctly accounting for constrained degrees of freedom (DoF).
• Validated across various systems, demonstrating robustness in complex scenarios.
• Identified kinetic energy equipartition breakdown as a sensitive indicator of numerical integration issues or insufficient equilibration.
• Demonstrated violation of equipartition between C and H atoms with rigid bonds at 2 fs time steps, signaling configurational overheating.

Conclusions:

• Accurate local temperature calculation in constrained molecular simulations is achievable through self-consistent DoF evaluation.
• The method provides a sensitive diagnostic tool for simulation quality, revealing issues like numerical integration errors or inadequate equilibration.
• Observed equipartition violations serve as a useful indicator of configurational overheating in simulations.