Local Temperature Measurement in Molecular Dynamics Simulations with Rigid Constraints

• Published in: Journal of chemical theory and computation Vol. 20; no. 23; pp. 10615 - 10624
• Main Authors: Sanderson, Stephen, Tee, Shern R., Searles, Debra J.
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 10.12.2024
• Subjects: Cartesian coordinates; Chemical bonds; Degrees of freedom; Energy; Equipartition theorem; Geometric constraints; Kinetic energy; Molecular dynamics; Numerical integration; Overheating; Simulation; Temperature; Temperature measurement; Thermodynamics

Constraining molecules in simulations (such as with constant bond lengths and/or angles) reduces their degrees of freedom (DoF), which in turn affects temperature calculations in those simulations. When local temperatures are measured, e.g., from a set of atoms in a subvolume or from velocities in o...