I am currently generating data by simulating a model of chemical system under different conditions (temperature) over time. In each simulation, the starting structure being modeled is exactly the same - only the temperature is different. The system is allowed to propagate over time and the length and number of observations in each simulation is identical. I would like to compare mean values e.g. distances between two atom under the different conditions. I have two questions:
Should I regard the two simulations I have (high and low temperature) as paired data. How would an analogous human study be treated (e.g. comparing the behaviour of a single human participant under during a 1 hour period under condition 1 and another 1 hour period after an extensive washout period - under condition 2)?
Since I effectively have two time series, what are the implications of the distance I want to measure being autocorrelated in some way?