Related Experiment Video
Updated: Jun 26, 2025

Simulating Temperature in a Soil Incubation Experiment
Published on: October 28, 2022
Uncertainties of predictions from temperature replica exchange simulations
Pavel Kříž1,2, Jan Beránek3, Vojtěch Spiwok3
1Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic.
Abstract:
Parallel tempering molecular dynamics simulation, also known as temperature replica exchange simulation, is a popular enhanced sampling method used to study biomolecular systems. This method makes it possible to calculate the free energy differences between states of the system for a series of temperatures. We developed a method to easily calculate the errors (standard errors or confidence intervals) of these predictions using a modified version of our recently introduced JumpCount method. The number of transitions between states (e.g., protein folding events) is counted for each temperature. This number of transitions, together with the temperature, fully determines the value of the standard error or the confidence interval of the free energy difference. We also address the issue of convergence in the situation where all replicas start from one state by developing an estimator of the equilibrium constant from simulations that are not fully equilibrated. The prerequisite of the method is the Markovianity of the process studied.
More Related Videos
10:22Split Point Analysis and Uncertainty Quantification of Thermal-Optical Organic/Elemental Carbon Measurements
Published on: September 7, 2019
09:18Laser-heating and Radiance Spectrometry for the Study of Nuclear Materials in Conditions Simulating a Nuclear Power Plant Accident
Published on: December 14, 2017
Related Concept Videos
Propagation of Uncertainty from Random Error
Random Error
Uncertainty in Measurement: Accuracy and Precision
Propagation of Uncertainty from Systematic Error
Uncertainty: Overview
Temperature Dependence on Reaction Rate
Atoms, molecules, or ions must collide before they can react with each other. Atoms must be close together to form chemical bonds. This premise is the basis for a theory that explains many observations regarding chemical kinetics, including factors affecting reaction rates.
The collision theory is based on the postulates that (i) the reaction rate is proportional to the rate of reactant collisions, (ii) the reacting species collide in an orientation allowing contact between...