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Local Temperature Measurement in Molecular Dynamics Simulations with Rigid Constraints.

Stephen Sanderson1, Shern R Tee1,2, Debra J Searles1,3,4

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Journal of Chemical Theory and Computation
|November 21, 2024
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Summary
This summary is machine-generated.

Accurately calculating local temperatures in simulations requires accounting for constrained degrees of freedom (DoF). This method correctly evaluates DoF for constrained atoms, ensuring reliable temperature calculations and detecting simulation artifacts.

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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.