This is slightly basic question using on statistical method on MD trjajectory.
I have done a MD simulation of protein molecule(P) for 30ns using 2 force fields(F1 and F2). I have taken the RMSD from both the trajectories(rmsd1, rmsd2 vectors) and computed the average RMSD ( avg1 and avg2)and standard deviations.(std1 and std2)
Now, if i want to compare these trajectories and show that the sample mean in RMSD(avg1 = avg2), what statistical analysis do I need to conduct .? By looking at the avg. values , the difference (avg1-avg2) is not much, is there any way(statistical) to show that the difference is not significant and is the comparison of sample means alone is sufficient or even I need to use the comparison of standard deviations ..?
please let me know if there are any other suggestions